US6617104B2

US6617104B2 - Predisposition to breast cancer by mutations at the ataxia-telangiectasia genetic locus

Info

Publication number: US6617104B2
Application number: US08/984,090
Authority: US
Inventors: Michael R. Swift
Original assignee: Individual
Current assignee: Individual
Priority date: 1996-12-03
Filing date: 1997-12-03
Publication date: 2003-09-09
Also published as: EP1012577A4; US20030148364A1; WO1998025125A2; EP1012577A2; WO1998025125A3; US20010021502A1; CA2273051A1

Abstract

The present invention relates generally to the field of human genetics. Specifically, the present invention relates to the discovery that some alleles of the A-T gene cause susceptibility to cancer, in particular breast cancer. More specifically, the present invention relates to germline mutations in the A-T gene and their use in the diagnosis of predisposition to breast cancer. The invention further relates to somatic mutations in the A-T gene in human breast cancer and their use in the diagnosis and prognosis of human breast cancer.

Description

CROSS REFERENCE TO RELATED APPLICATION

The present application is related to provisional patent application Serial No. 60/032,435, filed Dec. 3, 1996.

This invention was made with Government support under Grant Nos. CA 14235 and CA 50489 awarded by the National Cancer Institute, National Institutes of Health, Bethesda, Md. The United States Government has certain rights in the invention.

BACKGROUND OF THE INVENTION

The publications and other materials used herein to illuminate the background of the invention, and in particular, cases to provide additional details respecting the practice, are incorporated by reference, and for convenience are referenced in the following text by author and date and are listed alphabetically by author in the appended bibliography.

Breast cancer is a frequent cancer; there are approximately 183,00 new cases and 46,000 deaths from this cancer each year in the United States. It is the second most common cancer among women today, ranking only behind lung cancer. It has been estimated that the lifetime risk for a woman to develop breast cancer is about 1 in 9, although this figure must be interpreted with caution because not every women lives to age 100.

Breast cancer is treated by surgery, radiation therapy, and chemotherapy. New approaches to treatment have improved the survival of women with diagnosed breast cancer. Still, the most reliable approach to reducing mortality from this cancer is to detect it so early that treatment is more effective. It is well established that screening women by mammography beginning at age 50 leads to a substantial reduction in mortality from this cancer.

The concept that women in certain families were more likely to develop breast cancer than women in other families was noted in antiquity, observed several times in the ninteenth century, and established by family studies in the twentieth century. The observation of familial disposition to breast cancer had modest practical consequences because nothing could be done to decrease the risk of breast cancer for women in high risk families and there was no evidence that knowledge about this problem improved survival. Indeed, one could make a case that the awareness of familial predisposition led primarily to increased anxiety while having limited practical benefit.

In general, there are more cases of breast cancer among first and second degree relatives of breast cancer patients than would be expected according to the incidence of breast cancer in the general population. In a minority of families, the incidence of female breast cancer is so high that the pattern appears to follow a Mendelian autosomal dominent pattern of inheritance. Two genes, BRCA1 and BRCA2, have been shown responsible for the breast cancers in about two-thirds of families in which there are four or more cases of breast cancer. These genes have each been cloned and sequenced. A commercial laboratory, Myriad Genetics, now offers to test individuals to see if they carry BRCA1 or BRCA2, based on sequencing of the DNA from the individuals who are tested. Such testing will be valuable to those women—probably less than 1% of the population—who come from families in which the density of breast cancer is high.

The ataxia-telangiectasia (A-T) gene represents another approach to identifying a gene responsible for some breast cancers. This gene was first recognized because it causes a distinctive autosomal recessive syndrome characterized by cerebellar ataxia and oculocutaneous telangiectasia in children who have two copies of this gene (Swift, 1993). A great deal has been learned about the clinical features and laboratory findings in A-T since its description in the late 1950s. One of the most important facts to emerge was that patients with A-T (who will be called A-T homozygotes) developed cancer at a rate approximately 100-fold greater than children of the same age who do not have A-T (Morrell et al., 1986). It also became evident that the A-T gene makes homozygous patients and their cells many-fold more sensitive to the harmful effects of ionizing radiation. Lymphoid cancers predominate in childhood, while epithelial cancers including breast cancer are seen in adolescent and young adult A-T patients (Swift et al., 1990b).

Still, A-T homozygotes are rare and this gene might be of only theoretical interest except for the series of studies that suggested and now have confirmed that A-T heterozygotes, who constitute approximately 1.4% of the population, are also predisposed to cancer. The first evidence for this came from a study in the early 1970s in which it was shown that the cancer mortality in A-T blood relatives exceeded that of spouse controls in the same families by a statistically significant amount (Swift et al., 1976). This hypothesis was confirmed further by the retrospective analysis of 110 Caucasian A-T families in the United States in which there was a highly significant excess of cancer in the blood relatives when the incidence was compared to that in spouse controls. This study, published in 1987, provided the first evidence that the A-T gene predisposed to breast cancer. (Swift et al., 1987) Further support for the hypothesis was provided by a large scale prospective study of cancer incidence in A-T blood relatives and spouse controls published in 1991 (Swift et al., 1991), and by other smaller studies including two independent studies in Europe (Morrell et al., 1990; Peppard et al., 1988; Borresen et al., 1990).

The interpretation of these previous studies is limited by the facts that not all A-T blood relatives carry the A-T gene and by the inevitable question of how well the spouse controls are matched to the blood relatives. Though the study methods were standard, these limitations on interpretation remained. Further, findings from these earlier studies were characterized by several scientists as “a controversial suggestion,” (Kasten, 1995) “a possibility,” (Savitsky et al., 1995; Collins, 1996) or, “just a hypothesis” (Boice, 1995).

Thus, it is important to confirm that the A-T gene is associated with breast cancer using the best available genetic methods and identifying mutations in the A-T gene in families with breast cancer.

SUMMARY OF THE INVENTION

In accordance with the present invention, the hypothesis that A-T heterozygotes are predisposed to breast cancer has now been confirmed with unassailable rigor by collecting a group of female blood relatives with breast cancer in A-T families and testing DNA from each of these individuals to determine which of them carried the A-T gene. The method utilized highly polymorphic, tightly linked flanking markers (Gatti et al., 1994) and the index-test method (Swift et al., 1990a).

In addition, the association of the A-T gene with breast cancer is conclusively established by the identification of specific germline mutations in the A-T gene in families with breast cancer.

DETAILED DESCRIPTION OF THE INVENTION

Briefly, the hypothesis that female heterozygous carriers of the A-T gene are predisposed to breast cancer has now been established as described further below. In this test of the hypothesis, carriers of the A-T gene were identified by tracing the gene in families of A-T homozygous probands through tightly linked DNA markers. This is just one of the ways in which A-T heterozygotes can be identified. Indeed, in these carriers we have directly shown that they carry an A-T mutation in two of them, as described below.

More specifically, the hypothesis that A-T heterozygotes are predisposed to breast cancer was tested by the unbiased statistically powerful index-test method based on molecular genotyping. The A-T gene carrier status of 775 blood relatives in 99 A-T families was determined by tracing the A-T gene in each family through tightly linked flanking DNA markers. There were 33 women with breast cancer who could be genotyped; 25 of these were A-T heterozygotes, compared to 14.9 expected (odds ratio 3.8; 95% confidence limits 1.7-8.4; one-sided P=0.0001). This demonstrates that the A-T gene predisposes heterozygotes to breast cancer. For the 21 breast cancers with onset before age 60, the odds ratio was 2.9 (1.1-7.6; P=0.009) and for the 12 cases with onset at age 60 or older, the odds ratio was 6.4 (1.4-28.8; P=0.002). Thus the breast cancer risk for A-T heterozygous women is not limited to young women but appears even higher at older ages. Of all breast cancers in the United States, 6.6% may occur in women who are A-T heterozygotes. This proportion is several-fold greater than the estimated proportion of carriers of BRCA 1 mutations in breast cancer cases with onset at any age.

These new findings demonstrate that a test that reliably identifies heterozygous carriers of the A-T gene identifies individuals whose risk of breast cancer is substantially greater than the risk of non-carriers or the general population. The most efficient and least costly way to identify carriers of this gene may vary from situation to situation, according to the prior art. In one embodiment of the present invention, the least expensive, reliable way to identify gene carriers in families in which the A-T gene is known to be segregating is through tightly linked flanking markers, as in Examples 1 and 2 below.

In a second embodiment of the present invention, this predisposition to female breast cancer in the general population can be detected at present through testing an individual's DNA for mutations at the A-T gene locus. Any reliable laboratory or clinical test that will determine who carries the A-T gene will, according to the use proposed in this patent, be suitable for testing for cancer predisposition.

As an example of the second embodiment, heteroduplex analysis of two of the heterozygous carriers with breast cancer reported in the attached manuscript was used to identify two mutations. For heteroduplex analysis each exon of the A-T gene is amplified by the polymerase chain reaction (PCR) using as template genomic DNA from the test subject. The PCR product is then run on an MDE gel which detects heteroduplexes due to differences between the PCR products from the subject's two chromosomes. If there are no differences, then only a single band is seen and there is no sequence variation in that exon in that subject. When an additional band is seen, the PCR products are cloned so that DNA from each chromosome can be sequenced. The mutation is verified by comparison of the variant sequence to the known sequence of that exon in the A-T gene (Platzer et al., 1997). Further confirmation of the mutation is obtained by sequencing the same exon in close relatives of the subject.

The identification of these mutations conclusively confirms the involvement of the A-T gene in breast cancer. Specifically, one mutation is the nucleotide change ATC→TGAT at base 3245, codon 1082 in exon 24. A second mutation was a deletion of 150 basepairs beginning at nucleotide 8269 of codon 2757, leading to the deletion of exon 59. The first mutation predicts a truncation of the protein and the second predicts a deletion of 50 amino acids. These mutations and those noted herein are numbered with respect to the coding sequence of the A-T gene.

Alternatively, each exon of the A-T gene is amplified by PCR using primers based on the known sequence. The amplified exons are then sequenced using automated sequencers. In this manner, the exons of the A-T gene from families with breast cancer are sequenced until a mutation is found. The mutation is then confirmed in individual with breast cancer. Using this technique, an additional four mutations have been identified. One of these mutations is the deletion of 5 nucleotides beginning at nucleotide 2689 of exon 20. A second mutation is the deletion of AA beginning at nucleotide 1402 of exon 12. A third mutation is the deletion of GAAA beginning at nucleotide 1027 in exon 10. A fourth is the nucleotide change TTT→C at nucleotide 9003 in exon 65.

Also provided by the present invention are methods of detecting a polynucleotide comprising a portion of the A-T locus or its expression product in an analyte. Such methods may further comprise the step of amplifying the portion of the A-T locus, and may further include a step of providing a set of polynucleotides which are primers for amplification of said portion of the A-T locus. The method is useful for either diagnosis of the predisposition to cancer or the diagnosis or prognosis of cancer.

It is a discovery of the present invention that mutations in the A-T locus in the germline are indicative of a predisposition to breast cancer cancer. Finally, it is a discovery of the present invention that somatic mutations in the A-T locus are also associated with breast cancer, which represents an indicator of this cancer or of the prognosis of this cancer. The mutational events of the A-T locus can involve deletions, insertions and point mutations within the coding sequence and the non-coding sequence.

According to the diagnostic and prognostic method of the present invention, alteration of the wild-type A-T locus is detected. “Alteration of a wild-type gene” encompasses all forms of mutations including deletions, insertions and point mutations in the coding and noncoding regions. Deletions may be of the entire gene or of only a portion of the gene. Point mutations may result in stop codons, frameshift mutations or amino acid substitutions. Somatic mutations are those which occur only in certain tissues, e.g., in the tumor tissue, and are not inherited in the germline. Germline mutations can be found in any of a body's tissues and are inherited. If only a single allele is somatically mutated, an early neoplastic state is indicated. The finding of A-T mutations thus provides both diagnostic and prognostic information. An A-T allele which is not deleted (e.g., found on the sister chromosome to a chromosome carrying an A-T deletion) can be screened for other mutations, such as insertions, small deletions, and point mutations. It is believed that many mutations found in tumor tissues will be those leading to decreased expression of the A-T gene product. However, mutations leading to non-functional gene products would also lead to a cancerous state. Point mutational events may occur in regulatory regions, such as in the promoter of the gene, leading to loss or diminution of expression of the mRNA. Point mutations may also abolish proper RNA processing, leading to loss of expression of the A-T gene product, or to a decrease in mRNA stability or translation efficiency.

Useful diagnostic techniques include, but are not limited to direct DNA sequencing, PFGE analysis, allele-specific oligonucleotide (ASO), dot blot analysis and denaturing gradient el electrophoresis, as discussed in detail further below.

Predisposition to cancers, such as breast cancer, and the other cancers identified herein, can be ascertained by testing any tissue of a human for mutations of the A-T gene. For example, a person who has inherited a germline A-T mutation would be prone to develop cancers. This can be determined by testing DNA from any tissue of the person's body. Most simply, blood can be drawn and DNA extracted from the cells of the blood. In addition, prenatal diagnosis can be accomplished by testing fetal cells, placental cells or amniotic cells for mutations of the A-T gene. Alteration of a wild-type A-T allele, whether, for example, by point mutation or deletion, can be detected by any of the means discussed herein.

There are several methods that can be used to detect DNA sequence variation. Direct DNA sequencing, either manual sequencing or automated fluorescent sequencing can detect sequence variation. For a gene as large as A-T, manual sequencing is very labor-intensive, but under optimal conditions, mutations in the coding sequence of a gene are rarely missed. Another approach is the single-stranded conformation polymorphism assay (SSCA) (Orita et al., 1989). This method does not detect all sequence changes, especially if the DNA fragment size is greater than 200 bp, but can be optimized to detect most DNA sequence variation. The reduced detection sensitivity is a disadvantage, but the increased throughput possible with SSCA makes it an attractive, viable alternative to direct sequencing for mutation detection on a research basis. The fragments which have shifted mobility on SSCA gels are then sequenced to determine the exact nature of the DNA sequence variation. Other approaches based on the detection of mismatches between the two complementary DNA strands include clamped denaturing gel electrophoresis (CDGE) (Sheffield et al., 1991), heteroduplex analysis (HA) (White et al., 1992) and chemical mismatch cleavage (CMC) (Grompe et al., 1989). A review of currently available methods of detecting DNA sequence variation can be found in a recent review by Grompe (1993). Once a mutation is known, an allele specific detection approach such as allele specific oligonucleotide (ASO) hybridization can be utilized to rapidly screen large numbers of other samples for that same mutation. Such a technique can utilize probes which are labeled with gold nanoparticles to yield a visual color result (Elghanian et al., 1997).

In order to detect the alteration of the wild-type A-T gene in a tissue, it is helpful to isolate the tissue free from surrounding normal tissues. Means for enriching tissue preparation for tumor cells are known in the art. For example, the tissue may be isolated from paraffin or cryostat sections. Cancer cells may also be separated from normal cells by flow cytometry. These techniques, as well as other techniques for separating tumor cells from normal cells, are well known in the art. If the tumor tissue is highly contaminated with normal cells, detection of mutations is more difficult.

Detection of point mutations may be accomplished by molecular cloning of the A-T allele(s) and sequencing the allele(s) using techniques well known in the art. Alternatively, the gene sequences can be amplified directly from a genomic DNA preparation from the tumor tissue, using known techniques. The DNA sequence of the amplified sequences can then be determined.

There are six well known methods for a more complete, yet still indirect, test for confirming the presence of a susceptibility allele: 1) single stranded conformation analysis (SSCA) (Orita et al., 1989); 2) denaturing gradient gel electrophoresis (DGGE) (Wartell et al., 1990; Sheffield et al., 1989); 3) RNase protection assays (Finkelstein et al., 1990; Kinszler et al., 1991); 4) allele-specific oligonucleotides (ASOs) (Conner et al., 1983); 5) the use of proteins which recognize nucleotide mismatches, such as the E. coli mutS protein (Modrich, 1991); and 6) allele-specific PCR (Rano & Kidd, 1989). For allele-specific PCR, primers are used which hybridize at their 3′ ends to a particular A-T mutation. If the particular A-T mutation is not present, an amplification product is not observed. Amplification Refractory Mutation System (ARMS) can also be used, as disclosed in European Patent Application Publication No. 0332435 and in Newton et al., 1989. Insertions and deletions of genes can also be detected by cloning, sequencing and amplification. In addition, restriction fragment length polymorphism (RFLP) probes for the gene or surrounding marker genes can be used to score alteration of an allele or an insertion in a polymorphic fragment. Such a method is particularly useful for screening relatives of an affected individual for the presence of the A-T mutation found in that individual. Other techniques for detecting insertions and deletions as known in the art can be used.

In the first three methods (SSCA, DGGE and RNase protection assay), a new electrophoretic band appears. SSCA detects a band which migrates differentially because the sequence change causes a difference in single-strand, intramolecular base pairing. RNase protection involves cleavage of the mutant polynucleotide into two or more smaller fragments. DGGE detects differences in migration rates of mutant sequences compared to wild-type sequences, using a denaturing gradient gel. In an allele-specific oligonucleotide assay, an oligonucleotide is designed which detects a specific sequence, and the assay is performed by detecting the presence or absence of a hybridization signal. In the mutS assay, the protein binds only to sequences that contain a nucleotide mismatch in a heteroduplex between mutant and wild-type sequences.

Mismatches, according to the present invention, are hybridized nucleic acid duplexes in which the two strands are not 100% complementary. Lack of total homology may be due to deletions, insertions, inversions or substitutions. Mismatch detection can be used to detect point mutations in the gene or in its mRNA product. While these techniques are less sensitive than sequencing, they are simpler to perform on a large number of tumor samples. An example of a mismatch cleavage technique is the RNase protection method. In the practice of the present invention, the method involves the use of a labeled riboprobe which is complementary to the human wild-type A-T gene coding sequence. The riboprobe and either mRNA or DNA isolated from the tumor tissue are annealed (hybridized) together and subsequently digested with the enzyme RNase A which is able to detect some mismatches in a duplex RNA structure. If a mismatch is detected by RNase A, it cleaves at the site of the mismatch. Thus, when the annealed RNA preparation is separated on an electrophoretic gel matrix, if a mismatch has been detected and cleaved by RNase A, an RNA product will be seen which is smaller than the full length duplex RNA for the riboprobe and the mRNA or DNA. The riboprobe need not be the full length of the A-T mRNA or gene but can be a segment of either. If the riboprobe comprises only a segment of the A-T mRNA or gene, it will be desirable to use a number of these probes to screen the whole mRNA sequence for mismatches.

In similar fashion, DNA probes can be used to detect mismatches, through enzymatic or chemical cleavage. See, e.g., Cotton et al., 1988; Shenk et al., 1975; Novack et al., 1986. Alternatively, mismatches can be detected by shifts in the electrophoretic mobility of mismatched duplexes relative to matched duplexes. See, e.g., Cariello, 1988. With either riboprobes or DNA probes, the cellular mRNA or DNA which might contain a mutation can be amplified using PCR (see below) before hybridization.

The newly developed technique of nucleic acid analysis via microchip technology is also applicable to the present invention. In this technique, literally thousands of distinct oligonucleotide probes are built up in an array on a silicon chip. Nucleic acid to be analyzed is fluorescently labeled and hybridized to the probes on the chip. It is also possible to study nucleic acid-protein interactions using these nucleic acid microchips. Using this technique one can determine the presence of mutations or even sequence the nucleic acid being analyzed or one can measure expression levels of a gene of interest. The method is one of parallel processing of many, even thousands, of probes at once and can tremendously increase the rate of analysis. Several papers have been published which use this technique. Some of these are Hacia et al., 1996; Shoemaker et al., 1996; Chee et al., 1996; Lockhart et al., 1996; DeRisi et al., 1996; Lipshutz et al., 1995. This method has already been used to screen people for mutations in the breast cancer gene BRCA1 (Hacia et al., 1996). This new technology has been reviewed in a news article in Chemical and Engineering News (Borman, 1996) and been the subject of an editorial (Nature Genetics, 1996). Also see Fodor (1997).

DNA sequences of the A-T gene which have been amplified by use of PCR may also be screened using allele-specific probes. These probes are nucleic acid oligomers, each of which contains a region of the A-T gene sequence harboring a known mutation. For example, one oligomer may be about 30 nucleotides in length, corresponding to a portion of the A-T gene sequence. By use of a battery of such allele-specific probes, PCR amplification products can be screened to identify the presence of a previously identified mutation in the A-T gene. Hybridization of allele-specific probes with amplified A-T sequences can be performed, for example, on a nylon filter. Hybridization to a particular probe under stringent hybridization conditions indicates the presence of the same mutation in the tumor tissue as in the allele-specific probe.

Alteration of A-T mRNA expression can be detected by any techniques known in the art. These include Northern blot analysis, PCR amplification and RNase protection. Diminished mRNA expression indicates an alteration of the wild-type A-T gene. Alteration of wild-type A-T genes can also be detected by screening for alteration of wild-type A-T protein. For example, monoclonal antibodies immunoreactive with A-T can be used to screen a tissue. Lack of cognate antigen would indicate an A-T mutation. Antibodies specific for products of mutant alleles could also be used to detect mutant A-T gene product. Such immunological assays can be done in any convenient formats known in the art. These include Western blots, immunohistochemical assays and ELISA assays. Any means for detecting an altered A-T protein can be used to detect alteration of wild-type A-T genes. Functional assays, such as protein binding determinations, can be used. In addition, assays can be used which detect A-T biochemical function. Finding a mutant A-T gene product indicates alteration of a wild-type A-T gene.

Mutant A-T genes or gene products can also be detected in other human body samples, such as serum, stool, urine and sputum. The same techniques discussed above for detection of mutant A-T genes or gene products in tissues can be applied to other body samples. Cancer cells are sloughed off from tumors and appear in such body samples. In addition, the A-T gene product itself may be secreted into the extracellular space and found in these body samples even in the absence of cancer cells. By screening such body samples, a simple early diagnosis can be achieved for many types of cancers. In addition, the progress of chemotherapy or radiotherapy can be monitored more easily by testing such body samples for mutant A-T genes or gene products.

The methods of diagnosis of the present invention are applicable to any tumor in which A-T has a role in tumorigenesis. The diagnostic method of the present invention is useful for clinicians, so they can decide upon an appropriate course of treatment.

Primer pairs are useful for determination of the nucleotide sequence of a particular A-T allele using PCR. The pairs of single-stranded DNA primers can be annealed to sequences within or surrounding the A-T gene on chromosome 11q22-23 in order to prime amplifying DNA synthesis of the A-T gene itself. A complete set of these primers allows synthesis of all of the nucleotides of the A-T gene coding sequences, i.e., the exons. The set of primers preferably allows synthesis of both intron and exon sequences. Allele-specific primers can also be used. Such primers anneal only to particular A-T mutant alleles, and thus will only amplify a product in the presence of the mutant allele as a template.

In order to facilitate subsequent cloning of amplified sequences, primers may have restriction enzyme site sequences appended to their 5′ ends. Thus, all nucleotides of the primers are derived from A-T sequences or sequences adjacent to A-T, except for the few nucleotides necessary to form a restriction enzyme site. Such enzymes and sites are well known in the art. The primers themselves can be synthesized using techniques which are well known in the art. Generally, the primers can be made using oligonucleotide synthesizing machines which are commercially available. Given the sequence of the A-T open reading frame as set forth in Genbank accession number U33841 (Savitsky et al. 1995a; Savitsky et al., 1995b; Platzer et al., 1997), design of particular primers is well within the skill of the art.

The nucleic acid probes provided by the present invention are useful for a number of purposes. The probes can be used to detect PCR amplification products. They may also be used to detect mismatches with the A-T gene or mRNA using other techniques.

However, mutations which interfere with the function of the A-T protein are involved in the pathogenesis of cancer. Thus, the presence of an altered (or a mutant) A-T gene which produces a protein having a loss of function, or altered function, directly correlates to an increased risk of cancer. In order to detect a A-T gene mutation, a biological sample is prepared and analyzed for a difference between the sequence of the A-T allele being analyzed and the sequence of the wild-type A-T allele. Mutant A-T alleles can be initially identified by any of the techniques described above. The mutant alleles are then sequenced to identify the specific mutation of the particular mutant allele. Alternatively, mutant A-T alleles can be initially identified by identifying mutant (altered) A-T proteins, using conventional techniques. The mutant alleles are then sequenced to identify the specific mutation for each allele. The mutations, especially those which lead to an altered function of the A-T protein, are then used for the diagnostic and prognostic methods of the present invention.

Definitions

The present invention employs the following definitions:

“Amplification of Polynucleotides” utilizes methods such as the polymerase chain reaction (PCR), ligation amplification (or ligase chain reaction, LCR) and amplification methods based on the use of Q-beta replicase. These methods are well known and widely practiced in the art. See, e.g., U.S. Pat. Nos. 4,683,195 and 4,683,202 and Innis et al., 1990 (for PCR); and Wu et al., 1989a (for LCR). Reagents and hardware for conducting PCR are commercially available. Primers useful to amplify sequences from the A-T region are preferably complementary to, and hybridize specifically to sequences in the A-T region or in regions that flank a target region therein. A-T sequences generated by amplification may be sequenced directly. Alternatively, but less desirably, the amplified sequence(s) may be cloned prior to sequence analysis. A method for the direct cloning and sequence analysis of enzymatically amplified genomic segments has been described by Scharf, 1986.

“Analyte polynucleotide” and “analyte strand” refer to a single- or double-stranded polynucleotide which is suspected of containing a target sequence, and which may be present in a variety of types of samples, including biological samples.

“Antibodies.” The present invention also provides polyclonal and/or monoclonal antibodies and fragments thereof, and immunologic binding equivalents thereof, which are capable of specifically binding to the A-T polypeptides and fragments thereof or to polynucleotide sequences from the A-T region, particularly from the A-T locus or a portion thereof. The term “antibody” is used both to refer to a homogeneous molecular entity, or a mixture such as a serum product made up of a plurality of different molecular entities. Polypeptides may be prepared synthetically in a peptide synthesizer and coupled to a carrier molecule (e.g., keyhole limpet hemocyanin) and injected over several months into rabbits. Rabbit sera is tested for immunoreactivity to the A-T polypeptide or fragment. Monoclonal antibodies may be made by injecting mice with the protein polypeptides, fusion proteins or fragments thereof Monoclonal antibodies will be screened by ELISA and tested for specific immunoreactivity with A-T polypeptide or fragments thereof See, Harlow & Lane, 1988. These antibodies will be useful in assays as well as pharmaceuticals.

Once a sufficient quantity of desired polypeptide has been obtained, it may be used for various purposes. A typical use is the production of antibodies specific for binding. These antibodies may be either polyclonal or monoclonal, and may be produced by in vitro or in vivo techniques well known in the art. For production of polyclonal antibodies, an appropriate target immune system, typically mouse or rabbit, is selected. Substantially purified antigen is presented to the immune system in a fashion determined by methods appropriate for the animal and by other parameters well known to immunologists. Typical sites for injection are in footpads, intramuscularly, intraperitoneally, or intradermally. Of course, other species may be substituted for mouse or rabbit. Polyclonal antibodies are then purified using techniques known in the art, adjusted for the desired specificity.

An immunological response is usually assayed with an immunoassay. Normally, such immunoassays involve some purification of a source of antigen, for example, that produced by the same cells and in the same fashion as the antigen. A variety of immunoassay methods are well known in the art. See, e.g., Harlow & Lane, 1988, or Goding, 1986.

Monoclonal antibodies with affinities of 10⁻⁸M⁻¹or preferably 10⁻⁹to 10⁻¹⁰M⁻¹or stronger will typically be made by standard procedures as described, e.g., in Harlow & Lane, 1988 or Goding, 1986. Briefly, appropriate animals will be selected and the desired immunization protocol followed. After the appropriate period of time, the spleens of such animals are excised and individual spleen cells fused, typically, to immortalized myeloma cells under appropriate selection conditions. Thereafter, the cells are clonally separated and the supernatants of each clone tested for their production of an appropriate antibody specific for the desired region of the antigen.

Other suitable techniques involve in vitro exposure of lymphocytes to the antigenic polypeptides, or alternatively, to selection of libraries of antibodies in phage or similar vectors. See Huse et al., 1989. The polypeptides and antibodies of the present invention may be used with or without modification. Frequently, polypeptides and antibodies will be labeled by joining, either covalently or non-covalently, a substance which provides for a detectable signal. A wide variety of labels and conjugation techniques are known and are reported extensively in both the scientific and patent literature. Suitable labels include radionuclides, enzymes, substrates, cofactors, inhibitors, fluorescent agents, chemiluminescent agents, magnetic particles and the like. Patents teaching the use of such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149 and 4,366,241. Also, recombinant immunoglobulins may be produced (see U.S. Pat. No. 4,816,567).

“A-T allele” refers to normal alleles of the A-T locus as well as alleles carrying variations that predispose individuals to develop cancer of many sites including, for example, breast, ovarian, cancer. Such predisposing alleles are also called “A-T susceptibility alleles”.

“A-T locus,” “A-T gene,” “A-T Nucleic Acids” or “A-T Polynucleotide” each refer to polynucleotides, all of which are in the A-T region, that are likely to be expressed in normal tissue, certain alleles of which predispose an individual to develop breast, ovarian, cancers. Mutations at the A-T locus may be involved in the initiation and/or progression of other types of tumors. The locus is indicated in part by mutations that predispose individuals to develop cancer. These mutations fall within the A-T region. The A-T locus is intended to include coding sequences, intervening sequences and regulatory elements controlling transcription and/or translation. The A-T locus is intended to include all allelic variations of the DNA sequence.

A “biological sample” refers to a sample of tissue or fluid suspected of containing an analyte polynucleotide or polypeptide from an individual including, but not limited to, e.g., plasma, serum, spinal fluid, lymph fluid, the external sections of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, blood cells, tumors, organs, tissue and samples of in vitro cell culture constituents.

As used herein, the terms “diagnosing” or “prognosing,” as used in the context of neoplasia, are used to indicate 1) the classification of lesions as neoplasia, 2) the determination of the severity of the neoplasia, or 3) the monitoring of the disease progression, prior to, during and after treatment.

“Probes”. Polynucleotide sequence variants associated with A-T alleles which predispose to certain cancers or are associated with most cancers are detected by hybridization with a polynucleotide probe which forms a stable hybrid with that of the target sequence, under stringent to moderately stringent hybridization and wash conditions. If it is expected that the probes will be perfectly complementary to the target sequence, stringent conditions will be used. Hybridization stringency may be lessened if some mismatching is expected, for example, if variants are expected with the result that the probe will not be completely complementary. Conditions are chosen which rule out nonspecific/adventitious bindings, that is, which minimize noise. Since such indications identify neutral DNA polymorphisms as well as mutations, these indications need further analysis to demonstrate detection of an A-T susceptibility allele.

Probes for A-T alleles may be derived from the sequences of the A-T region or its cDNAs. The probes may be of any suitable length, which span all or a portion of the A-T region, and which allow specific hybridization to the A-T region. If the target sequence contains a sequence identical to that of the probe, the probes may be short, e.g., in the range of about 8-30 base pairs, since the hybrid will be relatively stable under even stringent conditions. If some degree of mismatch is expected with the probe, i.e., if it is suspected that the probe will hybridize to a variant region, a longer probe may be employed which hybridizes to the target sequence with the requisite specificity.

The probes will include an isolated polynucleotide attached to a label or reporter molecule and may be used to isolate other polynucleotide sequences, having sequence similarity by standard methods. For techniques for preparing and labeling probes see, e.g., Sambrook et al., 1989 or Ausubel et al., 1992. Other similar polynucleotides may be selected by using homologous polynucleotides. Alternatively, polynucleotides encoding these or similar polypeptides may be synthesized or selected by use of the redundancy in the genetic code. Various codon substitutions may be introduced, e.g., by silent changes (thereby producing various restriction sites) or to optimize expression for a particular system. Mutations may be introduced to modify the properties of the polypeptide, perhaps to change ligand-binding affinities, interchain affinities, or the polypeptide degradation or turnover rate.

Probes comprising synthetic oligonucleotides or other polynucleotides of the present invention may be derived from naturally occurring or recombinant single- or double-stranded polynucleotides, or be chemically synthesized. Probes may also be labeled by nick translation, Klenow fill-in reaction, or other methods known in the art.

Portions of the polynucleotide sequence having at least about eight nucleotides, usually at least about 15 nucleotides, and fewer than about 6 kb, usually fewer than about 1.0 kb, from a polynucleotide sequence encoding A-T are preferred as probes. The probes may also be used to determine whether mRNA encoding A-T is present in a cell or tissue.

“Target region” refers to a region of the nucleic acid which is amplified and/or detected. The term “target sequence” refers to a sequence with which a probe or primer will form a stable hybrid under desired conditions.

The practice of the present invention employs, unless otherwise indicated, conventional techniques of chemistry, molecular biology, microbiology, recombinant DNA, genetics, and immunology. See, e.g., Maniatis et al., 1982; Sambrook et al., 1989; Ausubel et al., 1992; Glover, 1985; Anand, 1992; Guthrie & Fink, 1991.

Methods of Use: Nucleic Acid Diagnosis and Diagnostic Kits

In order to detect the presence of a A-T allele predisposing an individual to cancer, a biological sample such as blood is prepared and analyzed for the presence or absence of susceptibility alleles of A-T. In order to detect the presence of neoplasia, the progression toward malignancy of a precursor lesion, or as a prognostic indicator, a biological sample of the lesion is prepared and analyzed for the presence or absence of mutant alleles of A-T. Results of these tests and interpretive information are returned to the health care provider for communication to the tested individual. Such diagnoses may be performed by diagnostic laboratories, or, alternatively, diagnostic kits are manufactured and sold to health care providers or to private individuals for self-diagnosis.

Initially, the screening method involves amplification of the relevant A-T sequences. In another preferred embodiment of the invention, the screening method involves a non-PCR based strategy. Such screening methods include two-step label amplification methodologies that are well known in the art. Both PCR and non-PCR based screening strategies can detect target sequences with a high level of sensitivity.

The most popular method used today is target amplification. Here, the target nucleic acid sequence is amplified with polymerases. One particularly preferred method using polymerase-driven amplification is the polymerase chain reaction (PCR). The polymerase chain reaction and other polymerase-driven amplification assays can achieve over a million-fold increase in copy number through the use of polymerase-driven amplification cycles. Once amplified, the resulting nucleic acid can be sequenced or used as a substrate for DNA probes.

When the probes are used to detect the presence of the target sequences (for example, in screening for cancer susceptibility), the biological sample to be analyzed, such as blood or serum, may be treated, if desired, to extract the nucleic acids. The sample nucleic acid may be prepared in various ways to facilitate detection of the target sequence; e.g. denaturation, restriction digestion, electrophoresis or dot blotting. The targeted region of the analyte nucleic acid usually must be at least partially single-stranded to form hybrids with the targeting sequence of the probe. If the sequence is naturally single-stranded, denaturation will not be required. However, if the sequence is double-stranded, the sequence will probably need to be denatured. Denaturation can be carried out by various techniques known in the art.

Analyte nucleic acid and probe are incubated under conditions which promote stable hybrid formation of the target sequence in the probe with the putative targeted sequence in the analyte. The region of the probes which is used to bind to the analyte can be made completely complementary to the targeted region of human chromosome 11q. Therefore, high stringency conditions are desirable in order to prevent false positives. However, conditions of high stringency are used only if the probes are complementary to regions of the chromosome which are unique in the genome. The stringency of hybridization is determined by a number of factors during hybridization and during the washing procedure, including temperature, ionic strength, base composition, probe length, and concentration of formamide. These factors are outlined in, for example, Maniatis et al., 1982 and Sambrook et al., 1989. Under certain circumstances, the formation of higher order hybrids, such as triplexes, quadraplexes, etc., may be desired to provide the means of detecting target sequences.

Detection, if any, of the resulting hybrid is usually accomplished by the use of labeled probes. Alternatively, the probe may be unlabeled, but may be detectable by specific binding with a ligand which is labeled, either directly or indirectly. Suitable labels, and methods for labeling probes and ligands are known in the art, and include, for example, radioactive labels which may be incorporated by known methods (e.g., nick translation, random priming or kinasing), biotin, fluorescent groups, chemiluminescent groups (e.g., dioxetanes, particularly triggered dioxetanes), enzymes, antibodies and the like. Variations of this basic scheme are known in the art, and include those variations that facilitate separation of the hybrids to be detected from extraneous materials and/or that amplify the signal from the labeled moiety. A number of these variations are reviewed in, e.g., Matthews & Kricka, 1988; Landegren et al., 1988; Mittlin, 1989; U.S. Pat. No. 4,868,105, and in EPO Publication No. 225,807.

As noted above, non-PCR based screening assays are also contemplated in this invention. This procedure hybridizes a nucleic acid probe (or an analog such as a methyl phosphonate backbone replacing the normal phosphodiester), to the low level DNA target. This probe may have an enzyme covalently linked to the probe, such that the covalent linkage does not interfere with the specificity of the hybridization. This enzyme-probe-conjugate-target nucleic acid complex can then be isolated away from the free probe enzyme conjugate and a substrate is added for enzyme detection. Enzymatic activity is observed as a change in color development or luminescent output resulting in a 10³-10⁶increase in sensitivity. For an example relating to the preparation of oligodeoxynucleotide-alkaline phosphatase conjugates and their use as hybridization probes see Jablonski et al., 1986.

Two-step label amplification methodologies are known in the art. These assays work on the principle that a small ligand (such as digoxigenin, biotin, or the like) is attached to a nucleic acid probe capable of specifically binding A-T. Allele specific probes are also contemplated within the scope of this invention.

In one example, the small ligand attached to the nucleic acid probe is specifically recognized by an antibody-enzyme conjugate. In one embodiment of this example, digoxigenin is attached to the nucleic acid probe. Hybridization is detected by an antibody-alkaline phosphatase conjugate which turns over a chemiluminescent substrate. For methods for labeling nucleic acid probes according to this embodiment see Martin et al., 1990. In a second example, the small ligand is recognized by a second ligand-enzyme conjugate that is capable of specifically complexing to the first ligand. A well known embodiment of this example is the biotin-avidin type of interactions. For methods for labeling nucleic acid probes and their use in biotin-avidin based assays see Rigby et al., 1977 and Nguyen et al., 1992.

It is also contemplated within the scope of this invention that the nucleic acid probe assays of this invention will employ a cocktail of nucleic acid probes capable of detecting A-T. Thus, in one example to detect the presence of A-T in a cell sample, more than one probe complementary to A-T is employed and in particular the number of different probes is alternatively 2, 3, or 5 different nucleic acid probe sequences. In another example, to detect the presence of mutations in the A-T gene sequence in a patient, more than one probe complementary to A-T is employed where the cocktail includes probes capable of binding to the allele-specific mutations identified in populations of patients with alterations in A-T. In this embodiment, any number of probes can be used, and will preferably include probes corresponding to the major gene mutations identified as predisposing an individual to breast cancer.

Methods of Use: Peptide Diagnosis and Diagnostic Kits

The neoplastic condition of lesions can also be detected on the basis of the alteration of wild-type A-T polypeptide. Such alterations can be determined by sequence analysis in accordance with conventional techniques. More preferably, antibodies (polyclonal or monoclonal) are used to detect differences in, or the absence of A-T peptides. The antibodies may be prepared as discussed above under the heading “Antibodies”. Other techniques for raising and purifying antibodies are well known in the art and any such techniques may be chosen to achieve the preparations claimed in this invention. In a preferred embodiment of the invention, antibodies will immunoprecipitate A-T proteins from solution as well as react with A-T protein on Western or immunoblots of polyacrylamide gels. In another preferred embodiment, antibodies will detect A-T proteins in paraffin or frozen tissue sections, using immunocytochemical techniques.

Preferred embodiments relating to methods for detecting A-T or its mutations include enzyme linked immunosorbent assays (ELISA), radioimmunoassays (RIA), immunoradiometric assays (IRMA) and immunoenzymatic assays (IEMA), including sandwich assays using monoclonal and/or polyclonal antibodies. Exemplary sandwich assays are described by David et al. in U.S. Pat. Nos. 4,376,110 and 4,486,530, hereby incorporated by reference.

The present invention is described by reference to the following Examples, which are offered by way of illustration and are not intended to limit the invention in any manner. Standard techniques well known in the art or the techniques specifically described below were utilized.

EXAMPLE 1 Methods

For genotyping, we obtained DNA samples (from blood or fixed tissue) from A-T homozygotes, who are the index individuals, their nuclear families, and all available blood relatives in their extended families. Informed consent was obtained from each study participant under a protocol approved by the New York Medical College Committee for the Protection of the Rights of Human Subjects. When DNA from a grandmother was not available, but DNA from her husband was, we genotyped the grandmother as a carrier when her husband was not, and vice versa. The requisite DNA samples for determining A-T gene carrier status were available for 99 out of the 261 A-T families participating in our continuing prospective study of mortality and cancer incidence.

Using standard procedures DNA was extracted from the blood lymphocytes of the A-T family members. From paraffin-embedded tissue we directly amplified without a xylene deparaffinization step or DNA extraction (Johnson et al., 1995). Genotyping was done through CA repeat markers D11S1778 and D11S1819 (Gatti et al., 1994) closely flanking the A-T gene locus. In 15 families in which haplotypes based on these two marker loci were not fully informative, D11S1818 (Gatti et al., 1994) and D11S384 (Lench et al., 1994) were also determined. The CA-strand primer was end-labeled with (γ-³²P)ATP and PCR was performed using standard conditions. The PCR products were analyzed on a 6% polyacrylamide sequencing gel and autoradiographs were read after 2-4 h exposure.

In two families there was a single recombination between D11S1778 and D11S1819; in both families the haplotype of the A-T chromosome was specified uniquely by D11S384, which shows zero recombination with the A-T locus, (Lench et al., 1994) and D11S1778. Neither of these recombinations affected the genotyping of breast cancer cases. Marker determinations, haplotypes and carrier status were reviewed independently three different times. Of the 775 A-T blood relatives (not obligate heterozygotes or homozygotes) who were genotyped in 99 A-T families, 390 were found to be carriers and 385 non-carriers. The expected numbers were 397.275 and 377.725 respectively.

In the 99 genotyped families, 43 female relatives with breast cancer were identified from our previously published studies, (Swift et al., 1987; Morrell et al., 1990; Swift et al., 1991) from the retrospective data for A-T families incorporated into this study subsequent to those studies, and from our ongoing prospective observation of A-T families. Hospital records from each presumed case were reviewed, prior to knowing the carrier status of the case, to confirm the diagnosis of breast cancer. Ten cases were excluded: two with lobular in situ carcinoma, six for which the marker loci did not amplify cleanly from their tissue sample, and two whose carrier status depended directly on that of another test subject with breast cancer.

Testing the association of A-T heterozygosity with breast cancer through the index-test method requires, in A-T families, determining the A-T gene carrier status of blood relatives with previously identified breast cancers. These test relatives cannot be homozygotes or obligate heterozygotes, whose genotypes are fixed. Both the A-T gene carrier status and relationship of each breast cancer case to the proband in each family were entered into a spreadsheet that calculated the odds ratio, 95% confidence limits, and t-statistic as previously described (Swift et al., 1990a). These calculations were based on comparing the observed number of carriers to the number expected on the basis of Mendelian inheritance and the population frequency of the A-T gene. The prior probability of heterozygosity for the A-T gene is approximately 0.67 for siblings, 0.5 for aunts and grandmothers, and 0.25 for first cousins of the homozygotes.

EXAMPLE 2 Association of A-T with Breast Cancer

In the 99 genotyped families we were able to determine the A-T gene carrier status for 26 women with breast cancer from blood samples, five from fixed tissues, and two others using DNA from the husbands. Thus, 33 breast cancer cases in 28 families were genotyped. Seventeen of these cases had been reported previously (Swift et al., 1987; Morrell et al., 1990; Swift et al., 1991). Only one of the six tissue samples for which PCR was unsuccessful came from an operation in 1980 or later, while four of the five successfully amplified specimens came from operations in 1980 or later (p=0.07).

Of the 33 women with invasive breast cancer, 25 were found to be A-T heterozygotes (Table 1). Ages at the onset of the cancers ranged from 31 to 77. These cancers were diagnosed between 1953 and 1995. Twelve of the breast cancers had occurred in aunts, 13 in grandmothers, five in great-aunts, and one in a sibling, a cousin, and a great-grandmother of an A-T proband. All eight of the non-carrier women, and 17 of the 25 A-T heterozygotes with breast cancer, were living as of Oct. 1, 1995. Five of the carrier women (20%), and two of the non-carriers (25%), had bilateral breast cancer.

TABLE 1

Age at diagnosis for genotyped breast cancers in A-T blood relatives

Age at diagnosis	A-T heterozygotes	Non-carriers

30-34	2	0
35-39	0	0
40-44	1	2
45-49	5	0
50-54	3	3
55-59	4	1
60-64	1	0
65-69	6	1
70-74	2	0
75-79	1	1
80+	0	0
Total	25	8

The expected number of A-T heterozygotes in the 33 breast cancer cases was 14.9. If the cancer incidence of carriers and that of non-carriers within the same families were equal, the odds ratio would be approximately one, indicating no association. Instead, for all breast cancers in this sample the odds ratio, which estimates the relative risk of carriers compared to non-carriers, was 3.8 (95% confidence limits 1.7-8.4; one-sided P=0.0001). For the 21 breast cancers with onset before age 60, the odds ratio was 2.9 (1.1-7.6; P=0.009) and for the 12 cases with onset at age 60 or older, the odds ratio was 6.4 (1.4-28.8; P=0.002).

The finding of 25 A-T gene carriers among 33 breast cancer cases in A-T families is compelling evidence that A-T heterozygotes are predisposed to breast cancer. There is no other explanation for this highly significant excess over the 14.9 expected on the basis of Mendelian inheritance and the A-T gene frequency. Since these data come from molecular genotyping, they are fully independent of all previous analyses of breast cancer incidence that compared blood relatives to spouse controls. While the comparison of blood relatives to spouse controls relies on how well these two groups are matched and on the fact that a high proportion of blood relatives are heterozygotes, gene carriers are identified directly with molecular genotyping in the index-test method.

The estimated relative risk, 3.8, of invasive breast cancer for A-T gene carriers compared to non-carriers is close to the most recent previous estimates from the prospective comparison of spouse controls with all blood relatives, 5.1, or with obligate heterozygotes, 3.8 (Swift et al., 1991). The large number of observed breast cancer cases in A-T blood relatives in their 30s, 40s, and 50s suggested previously that the excess breast cancer risk might be especially high for A-T heterozygotes in that age range (Swift et al., 1991). In contrast, molecular genotyping now shows that the relative risk above age 60 may be more than twice that of younger women.

The frequency of A-T heterozygotes in the United States population was estimated by maximum likelihood to be 1.4%, based on the number of families in which A-T homozygotes appeared in more than one sibship in an extended family (Swift et al., 1986). Based on this estimated heterozygote frequency and the estimated relative risks of 2.9 for breast cancers before age 60 and 6.4 for cases with onset after age 60, approximately 6.6% of all breast cancers in the United States occur in A-T heterozygotes [see Table 2]. If the risk of female A-T heterozygotes for breast cancer with onset from age 60 through age 79 is 6.4, then approximately 8.3% of all breast cancers arising in this age group occur in A-T heterozygotes.

TABLE 2

Estimated Frequencies

If the relative risk of breast cancer is 2.9 for cancers with onset before age

60, and the proportion of A-T heterozygotes in the general

population is 0.014,

then the ratio of breast cancer cases in A-T heterozygotes

to the total number of

cases with onset before age 60 is given by

\frac{2.9 \times 0.014}{(2.9 \times 0.014) + (1 \times 98.6)}

or 0.0395.

For breast cancers with onset at age 60 or older, the relative risk is 6.4

and the resulting proportion is 0.0833.

If 40%* of all breast cancers occur before age 60,

then 0.4 × 0.0395 = 0.01580

and 0.6 \times 0.0833 = \frac{0.04998}{0.06578},

which is the basis for the estimate that 6.6% of

all breast cancer cases occur in

A-T heterozygotes.

*The figure of 40% comes from New York State vital statistics.

Two genes, BRCA1 and BRCA2, that also predispose to breast cancer have been identified through molecular studies of families in which the risk of this cancer is very high (Szabo and King, 1995). The gene frequency of BRCA1 is much greater than that of BRCA2. In contrast to the A-T gene, the risk of breast cancer for BRCA1 gene carriers is highest at young ages; it has been estimated that the proportion of breast cancer cases in the general population due to BRCA1 is 5.3% for onset before age 40 years (Ford et al., 1995). For cases with onset ages 20-69, the estimated proportion is 1.7%. Since about 35% of all breast cancers occur after age 70 (New York State Cancer Registry, 1990), the proportion of BRCA1 carriers in all breast cancer cases is likely to be 1% or less, several fold lower than the estimated proportion of A-T gene carriers among all cases. A direct comparison of the impact of BRCA1, BRCA2, and the A-T gene on breast cancer incidence will be possible when population screening for mutations at these loci becomes practical.

The estimated relative risk of 3.8 is based on breast cancers that occurred in the United States between 1953 and 1995. However, the risk for A-T heterozygotes may vary with different environmental conditions or the genetic composition of a population. Since it will be valuable to attempt to replicate our findings as soon as possible, the risk estimate from our sample of persons of European origin could be compared to an independent estimate readily available through the A-T family registries already established in Europe (Pippard et al., 1988; Borressen et al., 1990; Chessa et al., 1994; Stoppa-Lyonnet et al., 1992). It will also be of great interest to collect family medical data and DNA samples in Africa and Asia to measure this risk in non-European populations.

Previously we found evidence that exposure to certain medical diagnostic X-ray procedures increased the risk of breast cancer for blood relatives in A-T families (Swift et al., 1987; Morrell et al., 1990). If breast cancer with onset above age 60 is more closely associated with A-T heterozygosity than earlier onset breast cancer, as our present data demonstrate, the difference may be explained by increasing exposure to medical diagnostic X-ray procedures with advancing age. Since some of the blood relatives with breast cancer in previous studies may have been non-carriers, we plan to re-examine this issue through a case-control analysis in which the X-ray exposures of identified carriers with breast cancer will be compared to that in matched carrier controls. We plan also to compare the histopathology or survival of A-T gene carriers with breast cancer to that of non-carriers within the same families. There are no data showing that bilateral breast cancer is more frequent among A-T heterozygotes than among non-carriers.

Unlike previous comparisons of blood relatives to spouse controls, these molecular findings cannot be explained by undetected confounders or unintended bias. No confounder can affect the result of the index-test method, since each individual's genotype is fixed at the time of conception. Unintended bias is implausible because the cases were selected, before genotyping, by the single criterion of having hospital record confirmation of breast cancer. The blood relatives did not know their own carrier status at the time they contributed blood samples. If carriers were more likely, because of some behavioral effect of the A-T gene, to contribute blood samples for genotyping than non-carriers, the proportion of carriers and non-carriers among all genotyped blood relatives in these 99 A-T families would have deviated significantly from the expected proportion. Further, it is not possible that more samples were available from breast cancer cases who are carriers because they survive longer, since the proportion of living cases was higher among the non-carriers. If there were an undetected breast cancer risk factor in the genotyped families, it would have affected breast cancer incidence in carriers and non-carriers equally and randomly. It is unlikely that the ability to PCR from stored fixed tissue influenced our result, since this appeared to be a function simply of the length of time specimens were stored.

Carrier determination through highly informative flanking haplotypes was reliable, since we detected no recombination between the closest markers and the A-T locus. Currently available methods for screening for mutations at this locus are tedious and costly, and seem to detect only 50-60% of all such mutations (Savitsky et al., 1995; Byrd et al., 1996; Gilad et al., 1996; Telatar et al., 1996). When population screening for A-T heterozygosity becomes practical, A-T heterozygotes found through such screening could be the index individuals for population based assessments, using the index-test method, of the risk of breast cancer for female A-T heterozygotes.

The A-T alleles segregating in the study families are a random sample of A-T alleles in the general population, since the only distinctive feature of the study families is that two heterozygotes met and had an offspring affected by ataxia-telangiectasia. Families in which this gene is segregating are ideal for testing hypothesized gene-disease associations, since there is natural matching for important risk factors between carriers and non-carriers in these families. It will be of considerable interest to measure the proportion of A-T heterozygotes among breast cancer patients in different populations when population screening is possible. However, comparing these proportions to the general population heterozygote frequency will be less reliable than the index-test method as a test of A-T heterozygote cancer predisposition because of the well-known difficulty in matching populations for confounders, such as ethnicity or social class, that affect both the A-T heterozygote frequency and breast cancer incidence.

Now that the excess risk of breast cancer for A-T heterozygotes has been measured using molecular genotyping and the index-test method, it is imperative to understand the molecular actions of the A-T gene and to identify the environmental and other genetic factors that interact with it to produce cancer.

EXAMPLE 3 Identification of Mutations by Heteroduplex Analysis

Heteroduplex analysis of two of the heterozygous carriers with breast cancer reported above was used to identify two mutations. For heteroduplex analysis each exon of the A-T gene was amplified by the polymerase chain reaction (PCR) using as template genomic DNA from the test subject and primers based on the known A-T gene sequence. The PCR product was then run on an MDE gel which detects heteroduplexes due to differences between the PCR products from the subject's two chromosomes. If there are no differences, then only a single band is seen and there is no sequence variation in that exon in that subject. When an additional band is seen, the PCR products were cloned so that DNA from each chromosome was sequenced. The mutation was verified by comparison of the variant sequence to the known sequence of that exon in the A-T gene (Savitsky et al., 1995a; Savitsky et al., 1995b; Platzer et al., 1997). Further confirmation of the mutation was obtained by sequencing the same exon in close relatives of the subject. With this technique, mutations were identified in the two heterozygotes. The first mutation seen was the nucleotide change ATC→TGAT at base 3245, codon 1082 in exon 24. The second mutation seen was a deletion of 150 basepairs beginning at nucleotide 8269 of codon 2757, leading to the deletion of exon 59. The first mutation predicts a truncation of the protein and the second predicts a deletion of 50 amino acids.

EXAMPLE 4 Identification of Mutations in Families by Sequencing

In this example, each exon of the A-T gene from A-T families with breast cancer was amplified by the polymerase chain reaction (PCR) using as template genomic DNA from the subject and primers based on the known A-T gene sequence. The amplified exons were then sequenced using automated sequencers. In this manner, the exons of the A-T gene from A-T families with breast cancer were sequenced until a mutation was found. The mutation is then confirmed in individual with breast cancer. Using this technique, four mutations in addition to those noted in Example 3 were identified and are set forth in Table 3. The mutations are with respect to the coding sequence of the A-T gene.

TABLE 3

A-T Gene Mutations in Families with Breast Cancer

Family	Exon	Nucleotide	Mutation

95	20	2689	5 bp deletion
104	12	1402	AA deletion
304	10	1027	GAAA deletion
397	65	9003	TTT → C

It will be appreciated that the methods and compositions of the instant invention can be incorporated in the form of a variety of embodiments, only a few of which are disclosed herein. It will be apparent to the artisan that other embodiments exist and do not depart from the spirit of the invention. Thus, the described embodiments are illustrative and should not be construed as restrictive.

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2

9196 base pairs

nucleic acid

single

linear

cDNA

CDS

1..9168

1 ATG AGT CTA GTA CTT AAT GAT CTG CTT ATC TGC TGC CGT CAA CTA GAA 48 Met Ser Leu Val Leu Asn Asp Leu Leu Ile Cys Cys Arg Gln Leu Glu 1 5 10 15 CAT GAT AGA GCT ACA GAA CGA AAG AAA GAA GTT GAG AAA TTT AAG CGC 96 His Asp Arg Ala Thr Glu Arg Lys Lys Glu Val Glu Lys Phe Lys Arg 20 25 30 CTG ATT CGA GAT CCT GAA ACA ATT AAA CAT CTA GAT CGG CAT TCA GAT 144 Leu Ile Arg Asp Pro Glu Thr Ile Lys His Leu Asp Arg His Ser Asp 35 40 45 TCC AAA CAA GGA AAA TAT TTG AAT TGG GAT GCT GTT TTT AGA TTT TTA 192 Ser Lys Gln Gly Lys Tyr Leu Asn Trp Asp Ala Val Phe Arg Phe Leu 50 55 60 CAG AAA TAT ATT CAG AAA GAA ACA GAA TGT CTG AGA ATA GCA AAA CCA 240 Gln Lys Tyr Ile Gln Lys Glu Thr Glu Cys Leu Arg Ile Ala Lys Pro 65 70 75 80 AAT GTA TCA GCC TCA ACA CAA GCC TCC AGG CAG AAA AAG ATG CAG GAA 288 Asn Val Ser Ala Ser Thr Gln Ala Ser Arg Gln Lys Lys Met Gln Glu 85 90 95 ATC AGT AGT TTG GTC AAA TAC TTC ATC AAA TGT GCA AAC AGA AGA GCA 336 Ile Ser Ser Leu Val Lys Tyr Phe Ile Lys Cys Ala Asn Arg Arg Ala 100 105 110 CCT AGG CTA AAA TGT CAA GAA CTC TTA AAT TAT ATC ATG GAT ACA GTG 384 Pro Arg Leu Lys Cys Gln Glu Leu Leu Asn Tyr Ile Met Asp Thr Val 115 120 125 AAA GAT TCA TCT AAT GGT GCT ATT TAC GGA GCT GAT TGT AGC AAC ATA 432 Lys Asp Ser Ser Asn Gly Ala Ile Tyr Gly Ala Asp Cys Ser Asn Ile 130 135 140 CTA CTC AAA GAC ATT CTT TCT GTG AGA AAA TAC TGG TGT GAA ATA TCT 480 Leu Leu Lys Asp Ile Leu Ser Val Arg Lys Tyr Trp Cys Glu Ile Ser 145 150 155 160 CAG CAA CAG TGG TTA GAA TTG TTC TCT GTG TAC TTC AGG CTC TAT CTG 528 Gln Gln Gln Trp Leu Glu Leu Phe Ser Val Tyr Phe Arg Leu Tyr Leu 165 170 175 AAA CCT TCA CAA GAT GTT CAT AGA GTT TTA GTG GCT AGA ATA ATT CAT 576 Lys Pro Ser Gln Asp Val His Arg Val Leu Val Ala Arg Ile Ile His 180 185 190 GCT GTT ACC AAA GGA TGC TGT TCT CAG ACT GAC GGA TTA AAT TCC AAA 624 Ala Val Thr Lys Gly Cys Cys Ser Gln Thr Asp Gly Leu Asn Ser Lys 195 200 205 TTT TTG GAC TTT TTT TCC AAG GCT ATT CAG TGT GCG AGA CAA GAA AAG 672 Phe Leu Asp Phe Phe Ser Lys Ala Ile Gln Cys Ala Arg Gln Glu Lys 210 215 220 AGC TCT TCA GGT CTA AAT CAT ATC TTA GCA GCT CTT ACT ATC TTC CTC 720 Ser Ser Ser Gly Leu Asn His Ile Leu Ala Ala Leu Thr Ile Phe Leu 225 230 235 240 AAG ACT TTG GCT GTC AAC TTT CGA ATT CGA GTG TGT GAA TTA GGA GAT 768 Lys Thr Leu Ala Val Asn Phe Arg Ile Arg Val Cys Glu Leu Gly Asp 245 250 255 GAA ATT CTT CCC ACT TTG CTT TAT ATT TGG ACT CAA CAT AGG CTT AAT 816 Glu Ile Leu Pro Thr Leu Leu Tyr Ile Trp Thr Gln His Arg Leu Asn 260 265 270 GAT TCT TTA AAA GAA GTC ATT ATT GAA TTA TTT CAA CTG CAA ATT TAT 864 Asp Ser Leu Lys Glu Val Ile Ile Glu Leu Phe Gln Leu Gln Ile Tyr 275 280 285 ATC CAT CAT CCG AAA GGA GCC AAA ACC CAA GAA AAA GGT GCT TAT GAA 912 Ile His His Pro Lys Gly Ala Lys Thr Gln Glu Lys Gly Ala Tyr Glu 290 295 300 TCA ACA AAA TGG AGA AGT ATT TTA TAC AAC TTA TAT GAT CTG CTA GTG 960 Ser Thr Lys Trp Arg Ser Ile Leu Tyr Asn Leu Tyr Asp Leu Leu Val 305 310 315 320 AAT GAG ATA AGT CAT ATA GGA AGT AGA GGA AAG TAT TCT TCA GGA TTT 1008 Asn Glu Ile Ser His Ile Gly Ser Arg Gly Lys Tyr Ser Ser Gly Phe 325 330 335 CGT AAT ATT GCC GTC AAA GAA AAT TTG ATT GAA TTG ATG GCA GAT ATC 1056 Arg Asn Ile Ala Val Lys Glu Asn Leu Ile Glu Leu Met Ala Asp Ile 340 345 350 TGT CAC CAG GTT TTT AAT GAA GAT ACC AGA TCC TTG GAG ATT TCT CAA 1104 Cys His Gln Val Phe Asn Glu Asp Thr Arg Ser Leu Glu Ile Ser Gln 355 360 365 TCT TAC ACT ACT ACA CAA AGA GAA TCT AGT GAT TAC AGT GTC CCT TGC 1152 Ser Tyr Thr Thr Thr Gln Arg Glu Ser Ser Asp Tyr Ser Val Pro Cys 370 375 380 AAA AGG AAG AAA ATA GAA CTA GGC TGG GAA GTA ATA AAA GAT CAC CTT 1200 Lys Arg Lys Lys Ile Glu Leu Gly Trp Glu Val Ile Lys Asp His Leu 385 390 395 400 CAG AAG TCA CAG AAT GAT TTT GAT CTT GTG CCT TGG CTA CAG ATT GCA 1248 Gln Lys Ser Gln Asn Asp Phe Asp Leu Val Pro Trp Leu Gln Ile Ala 405 410 415 ACC CAA TTA ATA TCA AAG TAT CCT GCA AGT TTA CCT AAC TGT GAG CTG 1296 Thr Gln Leu Ile Ser Lys Tyr Pro Ala Ser Leu Pro Asn Cys Glu Leu 420 425 430 TCT CCA TTA CTG ATG ATA CTA TCT CAG CTT CTA CCC CAA CAG CGA CAT 1344 Ser Pro Leu Leu Met Ile Leu Ser Gln Leu Leu Pro Gln Gln Arg His 435 440 445 GGG GAA CGT ACA CCA TAT GTG TTA CGA TGC CTT ACG GAA GTT GCA TTG 1392 Gly Glu Arg Thr Pro Tyr Val Leu Arg Cys Leu Thr Glu Val Ala Leu 450 455 460 TGT CAA GAC AAG AGG TCA AAC CTA GAA AGC TCA CAA AAG TCA GAT TTA 1440 Cys Gln Asp Lys Arg Ser Asn Leu Glu Ser Ser Gln Lys Ser Asp Leu 465 470 475 480 TTA AAA CTC TGG AAT AAA ATT TGG TGT ATT ACC TTT CGT GGT ATA AGT 1488 Leu Lys Leu Trp Asn Lys Ile Trp Cys Ile Thr Phe Arg Gly Ile Ser 485 490 495 TCT GAG CAA ATA CAA GCT GAA AAC TTT GGC TTA CTT GGA GCC ATA ATT 1536 Ser Glu Gln Ile Gln Ala Glu Asn Phe Gly Leu Leu Gly Ala Ile Ile 500 505 510 CAG GGT AGT TTA GTT GAG GTT GAC AGA GAA TTC TGG AAG TTA TTT ACT 1584 Gln Gly Ser Leu Val Glu Val Asp Arg Glu Phe Trp Lys Leu Phe Thr 515 520 525 GGG TCA GCC TGC AGA CCT TCA TGT CCT GCA GTA TGC TGT TTG ACT TTG 1632 Gly Ser Ala Cys Arg Pro Ser Cys Pro Ala Val Cys Cys Leu Thr Leu 530 535 540 GCA CTG ACC ACC AGT ATA GTT CCA GGA GCG GTA AAA ATG GGA ATA GAG 1680 Ala Leu Thr Thr Ser Ile Val Pro Gly Ala Val Lys Met Gly Ile Glu 545 550 555 560 CAA AAT ATG TGT GAA GTA AAT AGA AGC TTT TCT TTA AAG GAA TCA ATA 1728 Gln Asn Met Cys Glu Val Asn Arg Ser Phe Ser Leu Lys Glu Ser Ile 565 570 575 ATG AAA TGG CTC TTA TTC TAT CAG TTA GAG GGT GAC TTA GAA AAT AGC 1776 Met Lys Trp Leu Leu Phe Tyr Gln Leu Glu Gly Asp Leu Glu Asn Ser 580 585 590 ACA GAA GTG CCT CCA ATT CTT CAC AGT AAT TTT CCT CAT CTT GTA CTG 1824 Thr Glu Val Pro Pro Ile Leu His Ser Asn Phe Pro His Leu Val Leu 595 600 605 GAG AAA ATT CTT GTG AGT CTC ACT ATG AAA AAC TGT AAA GCT GCA ATG 1872 Glu Lys Ile Leu Val Ser Leu Thr Met Lys Asn Cys Lys Ala Ala Met 610 615 620 AAT TTT TTC CAA AGC GTG CCA GAA TGT GAA CAC CAC CAA AAA GAT AAA 1920 Asn Phe Phe Gln Ser Val Pro Glu Cys Glu His His Gln Lys Asp Lys 625 630 635 640 GAA GAA CTT TCA TTC TCA GAA GTA GAA GAA CTA TTT CTT CAG ACA ACT 1968 Glu Glu Leu Ser Phe Ser Glu Val Glu Glu Leu Phe Leu Gln Thr Thr 645 650 655 TTT GAC AAG ATG GAC TTT TTA ACC ATT GTG AGA GAA TGT GGT ATA GAA 2016 Phe Asp Lys Met Asp Phe Leu Thr Ile Val Arg Glu Cys Gly Ile Glu 660 665 670 AAG CAC CAG TCC AGT ATT GGC TTC TCT GTC CAC CAG AAT CTC AAG GAA 2064 Lys His Gln Ser Ser Ile Gly Phe Ser Val His Gln Asn Leu Lys Glu 675 680 685 TCA CTG GAT CGC TGT CTT CTG GGA TTA TCA GAA CAG CTT CTG AAT AAT 2112 Ser Leu Asp Arg Cys Leu Leu Gly Leu Ser Glu Gln Leu Leu Asn Asn 690 695 700 TAC TCA TCT GAG ATT ACA AAT TCA GAA ACT CTT GTC CGG TGT TCA CGT 2160 Tyr Ser Ser Glu Ile Thr Asn Ser Glu Thr Leu Val Arg Cys Ser Arg 705 710 715 720 CTT TTG GTG GGT GTC CTT GGC TGC TAC TGT TAC ATG GGT GTA ATA GCT 2208 Leu Leu Val Gly Val Leu Gly Cys Tyr Cys Tyr Met Gly Val Ile Ala 725 730 735 GAA GAG GAA GCA TAT AAG TCA GAA TTA TTC CAG AAA GCC AAC TCT CTA 2256 Glu Glu Glu Ala Tyr Lys Ser Glu Leu Phe Gln Lys Ala Asn Ser Leu 740 745 750 ATG CAA TGT GCA GGA GAA AGT ATC ACT CTG TTT AAA AAT AAG ACA AAT 2304 Met Gln Cys Ala Gly Glu Ser Ile Thr Leu Phe Lys Asn Lys Thr Asn 755 760 765 GAG GAA TTC AGA ATT GGT TCC TTG AGA AAT ATG ATG CAG CTA TGT ACA 2352 Glu Glu Phe Arg Ile Gly Ser Leu Arg Asn Met Met Gln Leu Cys Thr 770 775 780 CGT TGC TTG AGC AAC TGT ACC AAG AAG AGT CCA AAT AAG ATT GCA TCT 2400 Arg Cys Leu Ser Asn Cys Thr Lys Lys Ser Pro Asn Lys Ile Ala Ser 785 790 795 800 GGC TTT TTC CTG CGA TTG TTA ACA TCA AAG CTA ATG AAT GAC ATT GCA 2448 Gly Phe Phe Leu Arg Leu Leu Thr Ser Lys Leu Met Asn Asp Ile Ala 805 810 815 GAT ATT TGT AAA AGT TTA GCA TCC TTC ATC AAA AAG CCA TTT GAC CGT 2496 Asp Ile Cys Lys Ser Leu Ala Ser Phe Ile Lys Lys Pro Phe Asp Arg 820 825 830 GGA GAA GTA GAA TCA ATG GAA GAT GAT ACT AAT GGA AAT CTA ATG GAG 2544 Gly Glu Val Glu Ser Met Glu Asp Asp Thr Asn Gly Asn Leu Met Glu 835 840 845 GTG GAG GAT CAG TCA TCC ATG AAT CTA TTT AAC GAT TAC CCT GAT AGT 2592 Val Glu Asp Gln Ser Ser Met Asn Leu Phe Asn Asp Tyr Pro Asp Ser 850 855 860 AGT GTT AGT GAT GCA AAC GAA CCT GGA GAG AGC CAA AGT ACC ATA GGT 2640 Ser Val Ser Asp Ala Asn Glu Pro Gly Glu Ser Gln Ser Thr Ile Gly 865 870 875 880 GCC ATT AAT CCT TTA GCT GAA GAA TAT CTG TCA AAG CAA GAT CTA CTT 2688 Ala Ile Asn Pro Leu Ala Glu Glu Tyr Leu Ser Lys Gln Asp Leu Leu 885 890 895 TTC TTA GAC ATG CTC AAG TTC TTG TGT TTG TGT GTA ACT ACT GCT CAG 2736 Phe Leu Asp Met Leu Lys Phe Leu Cys Leu Cys Val Thr Thr Ala Gln 900 905 910 ACC AAT ACT GTG TCC TTT AGG GCA GCT GAT ATT CGG AGG AAA TTG TTA 2784 Thr Asn Thr Val Ser Phe Arg Ala Ala Asp Ile Arg Arg Lys Leu Leu 915 920 925 ATG TTA ATT GAT TCT AGC ACG CTA GAA CCT ACC AAA TCC CTC CAC CTG 2832 Met Leu Ile Asp Ser Ser Thr Leu Glu Pro Thr Lys Ser Leu His Leu 930 935 940 CAT ATG TAT CTA ATG CTT TTA AAG GAG CTT CCT GGA GAA GAG TAC CCC 2880 His Met Tyr Leu Met Leu Leu Lys Glu Leu Pro Gly Glu Glu Tyr Pro 945 950 955 960 TTG CCA ATG GAA GAT GTT CTT GAA CTT CTG AAA CCA CTA TCC AAT GTG 2928 Leu Pro Met Glu Asp Val Leu Glu Leu Leu Lys Pro Leu Ser Asn Val 965 970 975 TGT TCT TTG TAT CGT CGT GAC CAA GAT GTT TGT AAA ACT ATT TTA AAC 2976 Cys Ser Leu Tyr Arg Arg Asp Gln Asp Val Cys Lys Thr Ile Leu Asn 980 985 990 CAT GTC CTT CAT GTA GTG AAA AAC CTA GGT CAA AGC AAT ATG GAC TCT 3024 His Val Leu His Val Val Lys Asn Leu Gly Gln Ser Asn Met Asp Ser 995 1000 1005 GAG AAC ACA AGG GAT GCT CAA GGA CAG TTT CTT ACA GTA ATT GGA GCA 3072 Glu Asn Thr Arg Asp Ala Gln Gly Gln Phe Leu Thr Val Ile Gly Ala 1010 1015 1020 TTT TGG CAT CTA ACA AAG GAG AGG AAA TAT ATA TTC TCT GTA AGA ATG 3120 Phe Trp His Leu Thr Lys Glu Arg Lys Tyr Ile Phe Ser Val Arg Met 1025 1030 1035 1040 GCC CTA GTA AAT TGC CTT AAA ACT TTG CTT GAG GCT GAT CCT TAT TCA 3168 Ala Leu Val Asn Cys Leu Lys Thr Leu Leu Glu Ala Asp Pro Tyr Ser 1045 1050 1055 AAA TGG GCC ATT CTT AAT GTA ATG GGA AAA GAC TTT CCT GTA AAT GAA 3216 Lys Trp Ala Ile Leu Asn Val Met Gly Lys Asp Phe Pro Val Asn Glu 1060 1065 1070 GTA TTT ACA CAA TTT CTT GCT GAC AAT CAT CAC CAA GTT CGC ATG TTG 3264 Val Phe Thr Gln Phe Leu Ala Asp Asn His His Gln Val Arg Met Leu 1075 1080 1085 GCT GCA GAG TCA ATC AAT AGA TTG TTC CAG GAC ACG AAG GGA GAT TCT 3312 Ala Ala Glu Ser Ile Asn Arg Leu Phe Gln Asp Thr Lys Gly Asp Ser 1090 1095 1100 TCC AGG TTA CTG AAA GCA CTT CCT TTG AAG CTT CAG CAA ACA GCT TTT 3360 Ser Arg Leu Leu Lys Ala Leu Pro Leu Lys Leu Gln Gln Thr Ala Phe 1105 1110 1115 1120 GAA AAT GCA TAC TTG AAA GCT CAG GAA GGA ATG AGA GAA ATG TCC CAT 3408 Glu Asn Ala Tyr Leu Lys Ala Gln Glu Gly Met Arg Glu Met Ser His 1125 1130 1135 AGT GCT GAG AAC CCT GAA ACT TTG GAT GAA ATT TAT AAT AGA AAA TCT 3456 Ser Ala Glu Asn Pro Glu Thr Leu Asp Glu Ile Tyr Asn Arg Lys Ser 1140 1145 1150 GTT TTA CTG ACG TTG ATA GCT GTG GTT TTA TCC TGT AGC CCT ATC TGC 3504 Val Leu Leu Thr Leu Ile Ala Val Val Leu Ser Cys Ser Pro Ile Cys 1155 1160 1165 GAA AAA CAG GCT TTG TTT GCC CTG TGT AAA TCT GTG AAA GAG AAT GGA 3552 Glu Lys Gln Ala Leu Phe Ala Leu Cys Lys Ser Val Lys Glu Asn Gly 1170 1175 1180 TTA GAA CCT CAC CTT GTG AAA AAG GTT TTA GAG AAA GTT TCT GAA ACT 3600 Leu Glu Pro His Leu Val Lys Lys Val Leu Glu Lys Val Ser Glu Thr 1185 1190 1195 1200 TTT GGA TAT AGA CGT TTA GAA GAC TTT ATG GCA TCT CAT TTA GAT TAT 3648 Phe Gly Tyr Arg Arg Leu Glu Asp Phe Met Ala Ser His Leu Asp Tyr 1205 1210 1215 CTG GTT TTG GAA TGG CTA AAT CTT CAA GAT ACT GAA TAC AAC TTA TCT 3696 Leu Val Leu Glu Trp Leu Asn Leu Gln Asp Thr Glu Tyr Asn Leu Ser 1220 1225 1230 TCT TTT CCT TTT ATT TTA TTA AAC TAC ACA AAT ATT GAG GAT TTC TAT 3744 Ser Phe Pro Phe Ile Leu Leu Asn Tyr Thr Asn Ile Glu Asp Phe Tyr 1235 1240 1245 AGA TCT TGT TAT AAG GTT TTG ATT CCA CAT CTG GTG ATT AGA AGT CAT 3792 Arg Ser Cys Tyr Lys Val Leu Ile Pro His Leu Val Ile Arg Ser His 1250 1255 1260 TTT GAT GAG GTG AAG TCC ATT GCT AAT CAG ATT CAA GAG GAC TGG AAA 3840 Phe Asp Glu Val Lys Ser Ile Ala Asn Gln Ile Gln Glu Asp Trp Lys 1265 1270 1275 1280 AGT CTT CTA ACA GAC TGC TTT CCA AAG ATT CTT GTA AAT ATT CTT CCT 3888 Ser Leu Leu Thr Asp Cys Phe Pro Lys Ile Leu Val Asn Ile Leu Pro 1285 1290 1295 TAT TTT GCC TAT GAG GGT ACC AGA GAC AGT GGG ATG GCA CAG CAA AGA 3936 Tyr Phe Ala Tyr Glu Gly Thr Arg Asp Ser Gly Met Ala Gln Gln Arg 1300 1305 1310 GAG ACT GCT ACC AAG GTC TAT GAT ATG CTT AAA AGT GAA AAC TTA TTG 3984 Glu Thr Ala Thr Lys Val Tyr Asp Met Leu Lys Ser Glu Asn Leu Leu 1315 1320 1325 GGA AAA CAG ATT GAT CAC TTA TTC ATT AGT AAT TTA CCA GAG ATT GTG 4032 Gly Lys Gln Ile Asp His Leu Phe Ile Ser Asn Leu Pro Glu Ile Val 1330 1335 1340 GTG GAG TTA TTG ATG ACG TTA CAT GAG CCA GCA AAT TCT AGT GCC AGT 4080 Val Glu Leu Leu Met Thr Leu His Glu Pro Ala Asn Ser Ser Ala Ser 1345 1350 1355 1360 CAG AGC ACT GAC CTC TGT GAC TTT TCA GGG GAT TTG GAT CCT GCT CCT 4128 Gln Ser Thr Asp Leu Cys Asp Phe Ser Gly Asp Leu Asp Pro Ala Pro 1365 1370 1375 AAT CCA CCT CAT TTT CCA TCG CAT GTG ATT AAA GCA ACA TTT GCC TAT 4176 Asn Pro Pro His Phe Pro Ser His Val Ile Lys Ala Thr Phe Ala Tyr 1380 1385 1390 ATC AGC AAT TGT CAT AAA ACC AAG TTA AAA AGC ATT TTA GAA ATT CTT 4224 Ile Ser Asn Cys His Lys Thr Lys Leu Lys Ser Ile Leu Glu Ile Leu 1395 1400 1405 TCC AAA AGC CCT GAT TCC TAT CAG AAA ATT CTT CTT GCC ATA TGT GAG 4272 Ser Lys Ser Pro Asp Ser Tyr Gln Lys Ile Leu Leu Ala Ile Cys Glu 1410 1415 1420 CAA GCA GCT GAA ACA AAT AAT GTT TAT AAG AAG CAC AGA ATT CTT AAA 4320 Gln Ala Ala Glu Thr Asn Asn Val Tyr Lys Lys His Arg Ile Leu Lys 1425 1430 1435 1440 ATA TAT CAC CTG TTT GTT AGT TTA TTA CTG AAA GAT ATA AAA AGT GGC 4368 Ile Tyr His Leu Phe Val Ser Leu Leu Leu Lys Asp Ile Lys Ser Gly 1445 1450 1455 TTA GGA GGA GCT TGG GCC TTT GTT CTT CGA GAC GTT ATT TAT ACT TTG 4416 Leu Gly Gly Ala Trp Ala Phe Val Leu Arg Asp Val Ile Tyr Thr Leu 1460 1465 1470 ATT CAC TAT ATC AAC CAA AGG CCT TCT TGT ATC ATG GAT GTG TCA TTA 4464 Ile His Tyr Ile Asn Gln Arg Pro Ser Cys Ile Met Asp Val Ser Leu 1475 1480 1485 CGT AGC TTC TCC CTT TGT TGT GAC TTA TTA AGT CAG GTT TGC CAG ACA 4512 Arg Ser Phe Ser Leu Cys Cys Asp Leu Leu Ser Gln Val Cys Gln Thr 1490 1495 1500 GCC GTG ACT TAC TGT AAG GAT GCT CTA GAA AAC CAT CTT CAT GTT ATT 4560 Ala Val Thr Tyr Cys Lys Asp Ala Leu Glu Asn His Leu His Val Ile 1505 1510 1515 1520 GTT GGT ACA CTT ATA CCC CTT GTG TAT GAG CAG GTG GAG GTT CAG AAA 4608 Val Gly Thr Leu Ile Pro Leu Val Tyr Glu Gln Val Glu Val Gln Lys 1525 1530 1535 CAG GTA TTG GAC TTG TTG AAA TAC TTA GTG ATA GAT AAC AAG GAT AAT 4656 Gln Val Leu Asp Leu Leu Lys Tyr Leu Val Ile Asp Asn Lys Asp Asn 1540 1545 1550 GAA AAC CTC TAT ATC ACG ATT AAG CTT TTA GAT CCT TTT CCT GAC CAT 4704 Glu Asn Leu Tyr Ile Thr Ile Lys Leu Leu Asp Pro Phe Pro Asp His 1555 1560 1565 GTT GTT TTT AAG GAT TTG CGT ATT ACT CAG CAA AAA ATC AAA TAC AGT 4752 Val Val Phe Lys Asp Leu Arg Ile Thr Gln Gln Lys Ile Lys Tyr Ser 1570 1575 1580 AGA GGA CCC TTT TCA CTC TTG GAG GAA ATT AAC CAT TTT CTC TCA GTA 4800 Arg Gly Pro Phe Ser Leu Leu Glu Glu Ile Asn His Phe Leu Ser Val 1585 1590 1595 1600 AGT GTT TAT GAT GCA CTT CCA TTG ACA AGA CTT GAA GGA CTA AAG GAT 4848 Ser Val Tyr Asp Ala Leu Pro Leu Thr Arg Leu Glu Gly Leu Lys Asp 1605 1610 1615 CTT CGA AGA CAA CTG GAA CTA CAT AAA GAT CAG ATG GTG GAC ATT ATG 4896 Leu Arg Arg Gln Leu Glu Leu His Lys Asp Gln Met Val Asp Ile Met 1620 1625 1630 AGA GCT TCT CAG GAT AAT CCG CAA GAT GGG ATT ATG GTG AAA CTA GTT 4944 Arg Ala Ser Gln Asp Asn Pro Gln Asp Gly Ile Met Val Lys Leu Val 1635 1640 1645 GTC AAT TTG TTG CAG TTA TCC AAG ATG GCA ATA AAC CAC ACT GGT GAA 4992 Val Asn Leu Leu Gln Leu Ser Lys Met Ala Ile Asn His Thr Gly Glu 1650 1655 1660 AAA GAA GTT CTA GAG GCT GTT GGA AGC TGC TTG GGA GAA GTG GGT CCT 5040 Lys Glu Val Leu Glu Ala Val Gly Ser Cys Leu Gly Glu Val Gly Pro 1665 1670 1675 1680 ATA GAT TTC TCT ACC ATA GCT ATA CAA CAT AGT AAA GAT GCA TCT TAT 5088 Ile Asp Phe Ser Thr Ile Ala Ile Gln His Ser Lys Asp Ala Ser Tyr 1685 1690 1695 ACC AAG GCC CTT AAG TTA TTT GAA GAT AAA GAA CTT CAG TGG ACC TTC 5136 Thr Lys Ala Leu Lys Leu Phe Glu Asp Lys Glu Leu Gln Trp Thr Phe 1700 1705 1710 ATA ATG CTG ACC TAC CTG AAT AAC ACA CTG GTA GAA GAT TGT GTC AAA 5184 Ile Met Leu Thr Tyr Leu Asn Asn Thr Leu Val Glu Asp Cys Val Lys 1715 1720 1725 GTT CGA TCA GCA GCT GTT ACC TGT TTG AAA AAC ATT TTA GCC ACA AAG 5232 Val Arg Ser Ala Ala Val Thr Cys Leu Lys Asn Ile Leu Ala Thr Lys 1730 1735 1740 ACT GGA CAT AGT TTC TGG GAG ATT TAT AAG ATG ACA ACA GAT CCA ATG 5280 Thr Gly His Ser Phe Trp Glu Ile Tyr Lys Met Thr Thr Asp Pro Met 1745 1750 1755 1760 CTG GCC TAT CTA CAG CCT TTT AGA ACA TCA AGA AAA AAG TTT TTA GAA 5328 Leu Ala Tyr Leu Gln Pro Phe Arg Thr Ser Arg Lys Lys Phe Leu Glu 1765 1770 1775 GTA CCC AGA TTT GAC AAA GAA AAC CCT TTT GAA GGC CTG GAT GAT ATA 5376 Val Pro Arg Phe Asp Lys Glu Asn Pro Phe Glu Gly Leu Asp Asp Ile 1780 1785 1790 AAT CTG TGG ATT CCT CTA AGT GAA AAT CAT GAC ATT TGG ATA AAG ACA 5424 Asn Leu Trp Ile Pro Leu Ser Glu Asn His Asp Ile Trp Ile Lys Thr 1795 1800 1805 CTG ACT TGT GCT TTT TTG GAC AGT GGA GGC ACA AAA TGT GAA ATT CTT 5472 Leu Thr Cys Ala Phe Leu Asp Ser Gly Gly Thr Lys Cys Glu Ile Leu 1810 1815 1820 CAA TTA TTA AAG CCA ATG TGT GAA GTG AAA ACT GAC TTT TGT CAG ACT 5520 Gln Leu Leu Lys Pro Met Cys Glu Val Lys Thr Asp Phe Cys Gln Thr 1825 1830 1835 1840 GTA CTT CCA TAC TTG ATT CAT GAT ATT TTA CTC CAA GAT ACA AAT GAA 5568 Val Leu Pro Tyr Leu Ile His Asp Ile Leu Leu Gln Asp Thr Asn Glu 1845 1850 1855 TCA TGG AGA AAT CTG CTT TCT ACA CAT GTT CAG GGA TTT TTC ACC AGC 5616 Ser Trp Arg Asn Leu Leu Ser Thr His Val Gln Gly Phe Phe Thr Ser 1860 1865 1870 TGT CTT CGA CAC TTC TCG CAA ACG AGC CGA TCC ACA ACC CCT GCA AAC 5664 Cys Leu Arg His Phe Ser Gln Thr Ser Arg Ser Thr Thr Pro Ala Asn 1875 1880 1885 TTG GAT TCA GAG TCA GAG CAC TTT TTC CGA TGC TGT TTG GAT AAA AAA 5712 Leu Asp Ser Glu Ser Glu His Phe Phe Arg Cys Cys Leu Asp Lys Lys 1890 1895 1900 TCA CAA AGA ACA ATG CTT GCT GTT GTG GAC TAC ATG AGA AGA CAA AAG 5760 Ser Gln Arg Thr Met Leu Ala Val Val Asp Tyr Met Arg Arg Gln Lys 1905 1910 1915 1920 AGA CCT TCT TCA GGA ACA ATT TTT AAT GAT GCT TTC TGG CTG GAT TTA 5808 Arg Pro Ser Ser Gly Thr Ile Phe Asn Asp Ala Phe Trp Leu Asp Leu 1925 1930 1935 AAT TAT CTA GAA GTT GCC AAG GTA GCT CAG TCT TGT GCT GCT CAC TTT 5856 Asn Tyr Leu Glu Val Ala Lys Val Ala Gln Ser Cys Ala Ala His Phe 1940 1945 1950 ACA GCT TTA CTC TAT GCA GAA ATC TAT GCA GAT AAG AAA AGT ATG GAT 5904 Thr Ala Leu Leu Tyr Ala Glu Ile Tyr Ala Asp Lys Lys Ser Met Asp 1955 1960 1965 GAT CAA GAG AAA AGA AGT CTT GCA TTT GAA GAA GGA AGC CAG AGT ACA 5952 Asp Gln Glu Lys Arg Ser Leu Ala Phe Glu Glu Gly Ser Gln Ser Thr 1970 1975 1980 ACT ATT TCT AGC TTG AGT GAA AAA AGT AAA GAA GAA ACT GGA ATA AGT 6000 Thr Ile Ser Ser Leu Ser Glu Lys Ser Lys Glu Glu Thr Gly Ile Ser 1985 1990 1995 2000 TTA CAG GAT CTT CTC TTA GAA ATC TAC AGA AGT ATA GGG GAG CCA GAT 6048 Leu Gln Asp Leu Leu Leu Glu Ile Tyr Arg Ser Ile Gly Glu Pro Asp 2005 2010 2015 AGT TTG TAT GGC TGT GGT GGA GGG AAG ATG TTA CAA CCC ATT ACT AGA 6096 Ser Leu Tyr Gly Cys Gly Gly Gly Lys Met Leu Gln Pro Ile Thr Arg 2020 2025 2030 CTA CGA ACA TAT GAA CAC GAA GCA ATG TGG GGC AAA GCC CTA GTA ACA 6144 Leu Arg Thr Tyr Glu His Glu Ala Met Trp Gly Lys Ala Leu Val Thr 2035 2040 2045 TAT GAC CTC GAA ACA GCA ATC CCC TCA TCA ACA CGC CAG GCA GGA ATC 6192 Tyr Asp Leu Glu Thr Ala Ile Pro Ser Ser Thr Arg Gln Ala Gly Ile 2050 2055 2060 ATT CAG GCC TTG CAG AAT TTG GGA CTC TGC CAT ATT CTT TCC GTC TAT 6240 Ile Gln Ala Leu Gln Asn Leu Gly Leu Cys His Ile Leu Ser Val Tyr 2065 2070 2075 2080 TTA AAA GGA TTG GAT TAT GAA AAT AAA GAC TGG TGT CCT GAA CTA GAA 6288 Leu Lys Gly Leu Asp Tyr Glu Asn Lys Asp Trp Cys Pro Glu Leu Glu 2085 2090 2095 GAA CTT CAT TAC CAA GCA GCA TGG AGG AAT ATG CAG TGG GAC CAT TGC 6336 Glu Leu His Tyr Gln Ala Ala Trp Arg Asn Met Gln Trp Asp His Cys 2100 2105 2110 ACT TCC GTC AGC AAA GAA GTA GAA GGA ACC AGT TAC CAT GAA TCA TTG 6384 Thr Ser Val Ser Lys Glu Val Glu Gly Thr Ser Tyr His Glu Ser Leu 2115 2120 2125 TAC AAT GCT CTA CAA TCT CTA AGA GAC AGA GAA TTC TCT ACA TTT TAT 6432 Tyr Asn Ala Leu Gln Ser Leu Arg Asp Arg Glu Phe Ser Thr Phe Tyr 2130 2135 2140 GAA AGT CTC AAA TAT GCC AGA GTA AAA GAA GTG GAA GAG ATG TGT AAG 6480 Glu Ser Leu Lys Tyr Ala Arg Val Lys Glu Val Glu Glu Met Cys Lys 2145 2150 2155 2160 CGC AGC CTT GAG TCT GTG TAT TCG CTC TAT CCC ACA CTT AGC AGG TTG 6528 Arg Ser Leu Glu Ser Val Tyr Ser Leu Tyr Pro Thr Leu Ser Arg Leu 2165 2170 2175 CAG GCC ATT GGA GAG CTG GAA AGC ATT GGG GAG CTT TTC TCA AGA TCA 6576 Gln Ala Ile Gly Glu Leu Glu Ser Ile Gly Glu Leu Phe Ser Arg Ser 2180 2185 2190 GTC ACA CAT AGA CAA CTC TCT GAA GTA TAT ATT AAG TGG CAG AAA CAC 6624 Val Thr His Arg Gln Leu Ser Glu Val Tyr Ile Lys Trp Gln Lys His 2195 2200 2205 TCC CAG CTT CTC AAG GAC AGT GAT TTT AGT TTT CAG GAG CCT ATC ATG 6672 Ser Gln Leu Leu Lys Asp Ser Asp Phe Ser Phe Gln Glu Pro Ile Met 2210 2215 2220 GCT CTA CGC ACA GTC ATT TTG GAG ATC CTG ATG GAA AAG GAA ATG GAC 6720 Ala Leu Arg Thr Val Ile Leu Glu Ile Leu Met Glu Lys Glu Met Asp 2225 2230 2235 2240 AAC TCA CAA AGA GAA TGT ATT AAG GAC ATT CTC ACC AAA CAC CTT GTA 6768 Asn Ser Gln Arg Glu Cys Ile Lys Asp Ile Leu Thr Lys His Leu Val 2245 2250 2255 GAA CTC TCT ATA CTG GCC AGA ACT TTC AAG AAC ACT CAG CTC CCT GAA 6816 Glu Leu Ser Ile Leu Ala Arg Thr Phe Lys Asn Thr Gln Leu Pro Glu 2260 2265 2270 AGG GCA ATA TTT CAA ATT AAA CAG TAC AAT TCA GTT AGC TGT GGA GTC 6864 Arg Ala Ile Phe Gln Ile Lys Gln Tyr Asn Ser Val Ser Cys Gly Val 2275 2280 2285 TCT GAG TGG CAG CTG GAA GAA GCA CAA GTA TTC TGG GCA AAA AAG GAG 6912 Ser Glu Trp Gln Leu Glu Glu Ala Gln Val Phe Trp Ala Lys Lys Glu 2290 2295 2300 CAG AGT CTT GCC CTG AGT ATT CTC AAG CAA ATG ATC AAG AAG TTG GAT 6960 Gln Ser Leu Ala Leu Ser Ile Leu Lys Gln Met Ile Lys Lys Leu Asp 2305 2310 2315 2320 GCC AGC TGT GCA GCG AAC AAT CCC AGC CTA AAA CTT ACA TAC ACA GAA 7008 Ala Ser Cys Ala Ala Asn Asn Pro Ser Leu Lys Leu Thr Tyr Thr Glu 2325 2330 2335 TGT CTG AGG GTT TGT GGC AAC TGG TTA GCA GAA ACG TGC TTA GAA AAT 7056 Cys Leu Arg Val Cys Gly Asn Trp Leu Ala Glu Thr Cys Leu Glu Asn 2340 2345 2350 CCT GCG GTC ATC ATG CAG ACC TAT CTA GAA AAG GCA GTA GAA GTT GCT 7104 Pro Ala Val Ile Met Gln Thr Tyr Leu Glu Lys Ala Val Glu Val Ala 2355 2360 2365 GGA AAT TAT GAT GGA GAA AGT AGT GAT GAG CTA AGA AAT GGA AAA ATG 7152 Gly Asn Tyr Asp Gly Glu Ser Ser Asp Glu Leu Arg Asn Gly Lys Met 2370 2375 2380 AAG GCA TTT CTC TCA TTA GCC CGG TTT TCA GAT ACT CAA TAC CAA AGA 7200 Lys Ala Phe Leu Ser Leu Ala Arg Phe Ser Asp Thr Gln Tyr Gln Arg 2385 2390 2395 2400 ATT GAA AAC TAC ATG AAA TCA TCG GAA TTT GAA AAC AAG CAA GCT CTC 7248 Ile Glu Asn Tyr Met Lys Ser Ser Glu Phe Glu Asn Lys Gln Ala Leu 2405 2410 2415 CTG AAA AGA GCC AAA GAG GAA GTA GGT CTC CTT AGG GAA CAT AAA ATT 7296 Leu Lys Arg Ala Lys Glu Glu Val Gly Leu Leu Arg Glu His Lys Ile 2420 2425 2430 CAG ACA AAC AGA TAC ACA GTA AAG GTT CAG CGA GAG CTG GAG TTG GAT 7344 Gln Thr Asn Arg Tyr Thr Val Lys Val Gln Arg Glu Leu Glu Leu Asp 2435 2440 2445 GAA TTA GCC CTG CGT GCA CTG AAA GAG GAT CGT AAA CGC TTC TTA TGT 7392 Glu Leu Ala Leu Arg Ala Leu Lys Glu Asp Arg Lys Arg Phe Leu Cys 2450 2455 2460 AAA GCA GTT GAA AAT TAT ATC AAC TGC TTA TTA AGT GGA GAA GAA CAT 7440 Lys Ala Val Glu Asn Tyr Ile Asn Cys Leu Leu Ser Gly Glu Glu His 2465 2470 2475 2480 GAT ATG TGG GTA TTC CGG CTT TGT TCC CTC TGG CTT GAA AAT TCT GGA 7488 Asp Met Trp Val Phe Arg Leu Cys Ser Leu Trp Leu Glu Asn Ser Gly 2485 2490 2495 GTT TCT GAA GTC AAT GGC ATG ATG AAG AGA GAC GGA ATG AAG ATT CCA 7536 Val Ser Glu Val Asn Gly Met Met Lys Arg Asp Gly Met Lys Ile Pro 2500 2505 2510 ACA TAT AAA TTT TTG CCT CTT ATG TAC CAA TTG GCT GCT AGA ATG GGG 7584 Thr Tyr Lys Phe Leu Pro Leu Met Tyr Gln Leu Ala Ala Arg Met Gly 2515 2520 2525 ACC AAG ATG ATG GGA GGC CTA GGA TTT CAT GAA GTC CTC AAT AAT CTA 7632 Thr Lys Met Met Gly Gly Leu Gly Phe His Glu Val Leu Asn Asn Leu 2530 2535 2540 ATC TCT AGA ATT TCA ATG GAT CAC CCC CAT CAC ACT TTG TTT ATT ATA 7680 Ile Ser Arg Ile Ser Met Asp His Pro His His Thr Leu Phe Ile Ile 2545 2550 2555 2560 CTG GCC TTA GCA AAT GCA AAC AGA GAT GAA TTT CTG ACT AAA CCA GAG 7728 Leu Ala Leu Ala Asn Ala Asn Arg Asp Glu Phe Leu Thr Lys Pro Glu 2565 2570 2575 GTA GCC AGA AGA AGC AGA ATA ACT AAA AAT GTG CCT AAA CAA AGC TCT 7776 Val Ala Arg Arg Ser Arg Ile Thr Lys Asn Val Pro Lys Gln Ser Ser 2580 2585 2590 CAG CTT GAT GAG GAT CGA ACA GAG GCT GCA AAT AGA ATA ATA TGT ACT 7824 Gln Leu Asp Glu Asp Arg Thr Glu Ala Ala Asn Arg Ile Ile Cys Thr 2595 2600 2605 ATC AGA AGT AGG AGA CCT CAG ATG GTC AGA AGT GTT GAG GCA CTT TGT 7872 Ile Arg Ser Arg Arg Pro Gln Met Val Arg Ser Val Glu Ala Leu Cys 2610 2615 2620 GAT GCT TAT ATT ATA TTA GCA AAC TTA GAT GCC ACT CAG TGG AAG ACT 7920 Asp Ala Tyr Ile Ile Leu Ala Asn Leu Asp Ala Thr Gln Trp Lys Thr 2625 2630 2635 2640 CAG AGA AAA GGC ATA AAT ATT CCA GCA GAC CAG CCA ATT ACT AAA CTT 7968 Gln Arg Lys Gly Ile Asn Ile Pro Ala Asp Gln Pro Ile Thr Lys Leu 2645 2650 2655 AAG AAT TTA GAA GAT GTT GTT GTC CCT ACT ATG GAA ATT AAG GTG GAC 8016 Lys Asn Leu Glu Asp Val Val Val Pro Thr Met Glu Ile Lys Val Asp 2660 2665 2670 CAC ACA GGA GAA TAT GGA AAT CTG GTG ACT ATA CAG TCA TTT AAA GCA 8064 His Thr Gly Glu Tyr Gly Asn Leu Val Thr Ile Gln Ser Phe Lys Ala 2675 2680 2685 GAA TTT CGC TTA GCA GGA GGT GTA AAT TTA CCA AAA ATA ATA GAT TGT 8112 Glu Phe Arg Leu Ala Gly Gly Val Asn Leu Pro Lys Ile Ile Asp Cys 2690 2695 2700 GTA GGT TCC GAT GGC AAG GAG AGG AGA CAG CTT GTT AAG GGC CGT GAT 8160 Val Gly Ser Asp Gly Lys Glu Arg Arg Gln Leu Val Lys Gly Arg Asp 2705 2710 2715 2720 GAC CTG AGA CAA GAT GCT GTC ATG CAA CAG GTC TTC CAG ATG TGT AAT 8208 Asp Leu Arg Gln Asp Ala Val Met Gln Gln Val Phe Gln Met Cys Asn 2725 2730 2735 ACA TTA CTG CAG AGA AAC ACG GAA ACT AGG AAG AGG AAA TTA ACT ATC 8256 Thr Leu Leu Gln Arg Asn Thr Glu Thr Arg Lys Arg Lys Leu Thr Ile 2740 2745 2750 TGT ACT TAT AAG GTG GTT CCC CTC TCT CAG CGA AGT GGT GTT CTT GAA 8304 Cys Thr Tyr Lys Val Val Pro Leu Ser Gln Arg Ser Gly Val Leu Glu 2755 2760 2765 TGG TGC ACA GGA ACT GTC CCC ATT GGT GAA TTT CTT GTT AAC AAT GAA 8352 Trp Cys Thr Gly Thr Val Pro Ile Gly Glu Phe Leu Val Asn Asn Glu 2770 2775 2780 GAT GGT GCT CAT AAA AGA TAC AGG CCA AAT GAT TTC AGT GCC TTT CAG 8400 Asp Gly Ala His Lys Arg Tyr Arg Pro Asn Asp Phe Ser Ala Phe Gln 2785 2790 2795 2800 TGC CAA AAG AAA ATG ATG GAG GTG CAA AAA AAG TCT TTT GAA GAG AAA 8448 Cys Gln Lys Lys Met Met Glu Val Gln Lys Lys Ser Phe Glu Glu Lys 2805 2810 2815 TAT GAA GTC TTC ATG GAT GTT TGC CAA AAT TTT CAA CCA GTT TTC CGT 8496 Tyr Glu Val Phe Met Asp Val Cys Gln Asn Phe Gln Pro Val Phe Arg 2820 2825 2830 TAC TTC TGC ATG GAA AAA TTC TTG GAT CCA GCT ATT TGG TTT GAG AAG 8544 Tyr Phe Cys Met Glu Lys Phe Leu Asp Pro Ala Ile Trp Phe Glu Lys 2835 2840 2845 CGA TTG GCT TAT ACG CGC AGT GTA GCT ACT TCT TCT ATT GTT GGT TAC 8592 Arg Leu Ala Tyr Thr Arg Ser Val Ala Thr Ser Ser Ile Val Gly Tyr 2850 2855 2860 ATA CTT GGA CTT GGT GAT AGA CAT GTA CAG AAT ATC TTG ATA AAT GAG 8640 Ile Leu Gly Leu Gly Asp Arg His Val Gln Asn Ile Leu Ile Asn Glu 2865 2870 2875 2880 CAG TCA GCA GAA CTT GTA CAT ATA GAT CTA GGT GTT GCT TTT GAA CAG 8688 Gln Ser Ala Glu Leu Val His Ile Asp Leu Gly Val Ala Phe Glu Gln 2885 2890 2895 GGC AAA ATC CTT CCT ACT CCT GAG ACA GTT CCT TTT AGA CTC ACC AGA 8736 Gly Lys Ile Leu Pro Thr Pro Glu Thr Val Pro Phe Arg Leu Thr Arg 2900 2905 2910 GAT ATT GTG GAT GGC ATG GGC ATT ACG GGT GTT GAA GGT GTC TTC AGA 8784 Asp Ile Val Asp Gly Met Gly Ile Thr Gly Val Glu Gly Val Phe Arg 2915 2920 2925 AGA TGC TGT GAG AAA ACC ATG GAA GTG ATG AGA AAC TCT CAG GAA ACT 8832 Arg Cys Cys Glu Lys Thr Met Glu Val Met Arg Asn Ser Gln Glu Thr 2930 2935 2940 CTG TTA ACC ATT GTA GAG GTC CTT CTA TAT GAT CCA CTC TTT GAC TGG 8880 Leu Leu Thr Ile Val Glu Val Leu Leu Tyr Asp Pro Leu Phe Asp Trp 2945 2950 2955 2960 ACC ATG AAT CCT TTG AAA GCT TTG TAT TTA CAG CAG AGG CCG GAA GAT 8928 Thr Met Asn Pro Leu Lys Ala Leu Tyr Leu Gln Gln Arg Pro Glu Asp 2965 2970 2975 GAA ACT GAG CTT CAC CCT ACT CTG AAT GCA GAT GAC CAA GAA TGC AAA 8976 Glu Thr Glu Leu His Pro Thr Leu Asn Ala Asp Asp Gln Glu Cys Lys 2980 2985 2990 CGA AAT CTC AGT GAT ATT GAC CAG AGT TTC GAC AAA GTA GCT GAA CGT 9024 Arg Asn Leu Ser Asp Ile Asp Gln Ser Phe Asp Lys Val Ala Glu Arg 2995 3000 3005 GTC TTA ATG AGA CTA CAA GAG AAA CTG AAA GGA GTG GAA GAA GGC ACT 9072 Val Leu Met Arg Leu Gln Glu Lys Leu Lys Gly Val Glu Glu Gly Thr 3010 3015 3020 GTG CTC AGT GTT GGT GGA CAG GTG AAT TTG CTC ATA CAG CAG GCC ATA 9120 Val Leu Ser Val Gly Gly Gln Val Asn Leu Leu Ile Gln Gln Ala Ile 3025 3030 3035 3040 GAC CCC AAA AAT CTC AGC CGA CTT TTC CCA GGA TGG AAA GCT TGG GTG 9168 Asp Pro Lys Asn Leu Ser Arg Leu Phe Pro Gly Trp Lys Ala Trp Val 3045 3050 3055 TGATCTTCAG TATATGAATT ACCCTTTC 9196

3056 amino acids

amino acid

linear

protein

2 Met Ser Leu Val Leu Asn Asp Leu Leu Ile Cys Cys Arg Gln Leu Glu 1 5 10 15 His Asp Arg Ala Thr Glu Arg Lys Lys Glu Val Glu Lys Phe Lys Arg 20 25 30 Leu Ile Arg Asp Pro Glu Thr Ile Lys His Leu Asp Arg His Ser Asp 35 40 45 Ser Lys Gln Gly Lys Tyr Leu Asn Trp Asp Ala Val Phe Arg Phe Leu 50 55 60 Gln Lys Tyr Ile Gln Lys Glu Thr Glu Cys Leu Arg Ile Ala Lys Pro 65 70 75 80 Asn Val Ser Ala Ser Thr Gln Ala Ser Arg Gln Lys Lys Met Gln Glu 85 90 95 Ile Ser Ser Leu Val Lys Tyr Phe Ile Lys Cys Ala Asn Arg Arg Ala 100 105 110 Pro Arg Leu Lys Cys Gln Glu Leu Leu Asn Tyr Ile Met Asp Thr Val 115 120 125 Lys Asp Ser Ser Asn Gly Ala Ile Tyr Gly Ala Asp Cys Ser Asn Ile 130 135 140 Leu Leu Lys Asp Ile Leu Ser Val Arg Lys Tyr Trp Cys Glu Ile Ser 145 150 155 160 Gln Gln Gln Trp Leu Glu Leu Phe Ser Val Tyr Phe Arg Leu Tyr Leu 165 170 175 Lys Pro Ser Gln Asp Val His Arg Val Leu Val Ala Arg Ile Ile His 180 185 190 Ala Val Thr Lys Gly Cys Cys Ser Gln Thr Asp Gly Leu Asn Ser Lys 195 200 205 Phe Leu Asp Phe Phe Ser Lys Ala Ile Gln Cys Ala Arg Gln Glu Lys 210 215 220 Ser Ser Ser Gly Leu Asn His Ile Leu Ala Ala Leu Thr Ile Phe Leu 225 230 235 240 Lys Thr Leu Ala Val Asn Phe Arg Ile Arg Val Cys Glu Leu Gly Asp 245 250 255 Glu Ile Leu Pro Thr Leu Leu Tyr Ile Trp Thr Gln His Arg Leu Asn 260 265 270 Asp Ser Leu Lys Glu Val Ile Ile Glu Leu Phe Gln Leu Gln Ile Tyr 275 280 285 Ile His His Pro Lys Gly Ala Lys Thr Gln Glu Lys Gly Ala Tyr Glu 290 295 300 Ser Thr Lys Trp Arg Ser Ile Leu Tyr Asn Leu Tyr Asp Leu Leu Val 305 310 315 320 Asn Glu Ile Ser His Ile Gly Ser Arg Gly Lys Tyr Ser Ser Gly Phe 325 330 335 Arg Asn Ile Ala Val Lys Glu Asn Leu Ile Glu Leu Met Ala Asp Ile 340 345 350 Cys His Gln Val Phe Asn Glu Asp Thr Arg Ser Leu Glu Ile Ser Gln 355 360 365 Ser Tyr Thr Thr Thr Gln Arg Glu Ser Ser Asp Tyr Ser Val Pro Cys 370 375 380 Lys Arg Lys Lys Ile Glu Leu Gly Trp Glu Val Ile Lys Asp His Leu 385 390 395 400 Gln Lys Ser Gln Asn Asp Phe Asp Leu Val Pro Trp Leu Gln Ile Ala 405 410 415 Thr Gln Leu Ile Ser Lys Tyr Pro Ala Ser Leu Pro Asn Cys Glu Leu 420 425 430 Ser Pro Leu Leu Met Ile Leu Ser Gln Leu Leu Pro Gln Gln Arg His 435 440 445 Gly Glu Arg Thr Pro Tyr Val Leu Arg Cys Leu Thr Glu Val Ala Leu 450 455 460 Cys Gln Asp Lys Arg Ser Asn Leu Glu Ser Ser Gln Lys Ser Asp Leu 465 470 475 480 Leu Lys Leu Trp Asn Lys Ile Trp Cys Ile Thr Phe Arg Gly Ile Ser 485 490 495 Ser Glu Gln Ile Gln Ala Glu Asn Phe Gly Leu Leu Gly Ala Ile Ile 500 505 510 Gln Gly Ser Leu Val Glu Val Asp Arg Glu Phe Trp Lys Leu Phe Thr 515 520 525 Gly Ser Ala Cys Arg Pro Ser Cys Pro Ala Val Cys Cys Leu Thr Leu 530 535 540 Ala Leu Thr Thr Ser Ile Val Pro Gly Ala Val Lys Met Gly Ile Glu 545 550 555 560 Gln Asn Met Cys Glu Val Asn Arg Ser Phe Ser Leu Lys Glu Ser Ile 565 570 575 Met Lys Trp Leu Leu Phe Tyr Gln Leu Glu Gly Asp Leu Glu Asn Ser 580 585 590 Thr Glu Val Pro Pro Ile Leu His Ser Asn Phe Pro His Leu Val Leu 595 600 605 Glu Lys Ile Leu Val Ser Leu Thr Met Lys Asn Cys Lys Ala Ala Met 610 615 620 Asn Phe Phe Gln Ser Val Pro Glu Cys Glu His His Gln Lys Asp Lys 625 630 635 640 Glu Glu Leu Ser Phe Ser Glu Val Glu Glu Leu Phe Leu Gln Thr Thr 645 650 655 Phe Asp Lys Met Asp Phe Leu Thr Ile Val Arg Glu Cys Gly Ile Glu 660 665 670 Lys His Gln Ser Ser Ile Gly Phe Ser Val His Gln Asn Leu Lys Glu 675 680 685 Ser Leu Asp Arg Cys Leu Leu Gly Leu Ser Glu Gln Leu Leu Asn Asn 690 695 700 Tyr Ser Ser Glu Ile Thr Asn Ser Glu Thr Leu Val Arg Cys Ser Arg 705 710 715 720 Leu Leu Val Gly Val Leu Gly Cys Tyr Cys Tyr Met Gly Val Ile Ala 725 730 735 Glu Glu Glu Ala Tyr Lys Ser Glu Leu Phe Gln Lys Ala Asn Ser Leu 740 745 750 Met Gln Cys Ala Gly Glu Ser Ile Thr Leu Phe Lys Asn Lys Thr Asn 755 760 765 Glu Glu Phe Arg Ile Gly Ser Leu Arg Asn Met Met Gln Leu Cys Thr 770 775 780 Arg Cys Leu Ser Asn Cys Thr Lys Lys Ser Pro Asn Lys Ile Ala Ser 785 790 795 800 Gly Phe Phe Leu Arg Leu Leu Thr Ser Lys Leu Met Asn Asp Ile Ala 805 810 815 Asp Ile Cys Lys Ser Leu Ala Ser Phe Ile Lys Lys Pro Phe Asp Arg 820 825 830 Gly Glu Val Glu Ser Met Glu Asp Asp Thr Asn Gly Asn Leu Met Glu 835 840 845 Val Glu Asp Gln Ser Ser Met Asn Leu Phe Asn Asp Tyr Pro Asp Ser 850 855 860 Ser Val Ser Asp Ala Asn Glu Pro Gly Glu Ser Gln Ser Thr Ile Gly 865 870 875 880 Ala Ile Asn Pro Leu Ala Glu Glu Tyr Leu Ser Lys Gln Asp Leu Leu 885 890 895 Phe Leu Asp Met Leu Lys Phe Leu Cys Leu Cys Val Thr Thr Ala Gln 900 905 910 Thr Asn Thr Val Ser Phe Arg Ala Ala Asp Ile Arg Arg Lys Leu Leu 915 920 925 Met Leu Ile Asp Ser Ser Thr Leu Glu Pro Thr Lys Ser Leu His Leu 930 935 940 His Met Tyr Leu Met Leu Leu Lys Glu Leu Pro Gly Glu Glu Tyr Pro 945 950 955 960 Leu Pro Met Glu Asp Val Leu Glu Leu Leu Lys Pro Leu Ser Asn Val 965 970 975 Cys Ser Leu Tyr Arg Arg Asp Gln Asp Val Cys Lys Thr Ile Leu Asn 980 985 990 His Val Leu His Val Val Lys Asn Leu Gly Gln Ser Asn Met Asp Ser 995 1000 1005 Glu Asn Thr Arg Asp Ala Gln Gly Gln Phe Leu Thr Val Ile Gly Ala 1010 1015 1020 Phe Trp His Leu Thr Lys Glu Arg Lys Tyr Ile Phe Ser Val Arg Met 1025 1030 1035 1040 Ala Leu Val Asn Cys Leu Lys Thr Leu Leu Glu Ala Asp Pro Tyr Ser 1045 1050 1055 Lys Trp Ala Ile Leu Asn Val Met Gly Lys Asp Phe Pro Val Asn Glu 1060 1065 1070 Val Phe Thr Gln Phe Leu Ala Asp Asn His His Gln Val Arg Met Leu 1075 1080 1085 Ala Ala Glu Ser Ile Asn Arg Leu Phe Gln Asp Thr Lys Gly Asp Ser 1090 1095 1100 Ser Arg Leu Leu Lys Ala Leu Pro Leu Lys Leu Gln Gln Thr Ala Phe 1105 1110 1115 1120 Glu Asn Ala Tyr Leu Lys Ala Gln Glu Gly Met Arg Glu Met Ser His 1125 1130 1135 Ser Ala Glu Asn Pro Glu Thr Leu Asp Glu Ile Tyr Asn Arg Lys Ser 1140 1145 1150 Val Leu Leu Thr Leu Ile Ala Val Val Leu Ser Cys Ser Pro Ile Cys 1155 1160 1165 Glu Lys Gln Ala Leu Phe Ala Leu Cys Lys Ser Val Lys Glu Asn Gly 1170 1175 1180 Leu Glu Pro His Leu Val Lys Lys Val Leu Glu Lys Val Ser Glu Thr 1185 1190 1195 1200 Phe Gly Tyr Arg Arg Leu Glu Asp Phe Met Ala Ser His Leu Asp Tyr 1205 1210 1215 Leu Val Leu Glu Trp Leu Asn Leu Gln Asp Thr Glu Tyr Asn Leu Ser 1220 1225 1230 Ser Phe Pro Phe Ile Leu Leu Asn Tyr Thr Asn Ile Glu Asp Phe Tyr 1235 1240 1245 Arg Ser Cys Tyr Lys Val Leu Ile Pro His Leu Val Ile Arg Ser His 1250 1255 1260 Phe Asp Glu Val Lys Ser Ile Ala Asn Gln Ile Gln Glu Asp Trp Lys 1265 1270 1275 1280 Ser Leu Leu Thr Asp Cys Phe Pro Lys Ile Leu Val Asn Ile Leu Pro 1285 1290 1295 Tyr Phe Ala Tyr Glu Gly Thr Arg Asp Ser Gly Met Ala Gln Gln Arg 1300 1305 1310 Glu Thr Ala Thr Lys Val Tyr Asp Met Leu Lys Ser Glu Asn Leu Leu 1315 1320 1325 Gly Lys Gln Ile Asp His Leu Phe Ile Ser Asn Leu Pro Glu Ile Val 1330 1335 1340 Val Glu Leu Leu Met Thr Leu His Glu Pro Ala Asn Ser Ser Ala Ser 1345 1350 1355 1360 Gln Ser Thr Asp Leu Cys Asp Phe Ser Gly Asp Leu Asp Pro Ala Pro 1365 1370 1375 Asn Pro Pro His Phe Pro Ser His Val Ile Lys Ala Thr Phe Ala Tyr 1380 1385 1390 Ile Ser Asn Cys His Lys Thr Lys Leu Lys Ser Ile Leu Glu Ile Leu 1395 1400 1405 Ser Lys Ser Pro Asp Ser Tyr Gln Lys Ile Leu Leu Ala Ile Cys Glu 1410 1415 1420 Gln Ala Ala Glu Thr Asn Asn Val Tyr Lys Lys His Arg Ile Leu Lys 1425 1430 1435 1440 Ile Tyr His Leu Phe Val Ser Leu Leu Leu Lys Asp Ile Lys Ser Gly 1445 1450 1455 Leu Gly Gly Ala Trp Ala Phe Val Leu Arg Asp Val Ile Tyr Thr Leu 1460 1465 1470 Ile His Tyr Ile Asn Gln Arg Pro Ser Cys Ile Met Asp Val Ser Leu 1475 1480 1485 Arg Ser Phe Ser Leu Cys Cys Asp Leu Leu Ser Gln Val Cys Gln Thr 1490 1495 1500 Ala Val Thr Tyr Cys Lys Asp Ala Leu Glu Asn His Leu His Val Ile 1505 1510 1515 1520 Val Gly Thr Leu Ile Pro Leu Val Tyr Glu Gln Val Glu Val Gln Lys 1525 1530 1535 Gln Val Leu Asp Leu Leu Lys Tyr Leu Val Ile Asp Asn Lys Asp Asn 1540 1545 1550 Glu Asn Leu Tyr Ile Thr Ile Lys Leu Leu Asp Pro Phe Pro Asp His 1555 1560 1565 Val Val Phe Lys Asp Leu Arg Ile Thr Gln Gln Lys Ile Lys Tyr Ser 1570 1575 1580 Arg Gly Pro Phe Ser Leu Leu Glu Glu Ile Asn His Phe Leu Ser Val 1585 1590 1595 1600 Ser Val Tyr Asp Ala Leu Pro Leu Thr Arg Leu Glu Gly Leu Lys Asp 1605 1610 1615 Leu Arg Arg Gln Leu Glu Leu His Lys Asp Gln Met Val Asp Ile Met 1620 1625 1630 Arg Ala Ser Gln Asp Asn Pro Gln Asp Gly Ile Met Val Lys Leu Val 1635 1640 1645 Val Asn Leu Leu Gln Leu Ser Lys Met Ala Ile Asn His Thr Gly Glu 1650 1655 1660 Lys Glu Val Leu Glu Ala Val Gly Ser Cys Leu Gly Glu Val Gly Pro 1665 1670 1675 1680 Ile Asp Phe Ser Thr Ile Ala Ile Gln His Ser Lys Asp Ala Ser Tyr 1685 1690 1695 Thr Lys Ala Leu Lys Leu Phe Glu Asp Lys Glu Leu Gln Trp Thr Phe 1700 1705 1710 Ile Met Leu Thr Tyr Leu Asn Asn Thr Leu Val Glu Asp Cys Val Lys 1715 1720 1725 Val Arg Ser Ala Ala Val Thr Cys Leu Lys Asn Ile Leu Ala Thr Lys 1730 1735 1740 Thr Gly His Ser Phe Trp Glu Ile Tyr Lys Met Thr Thr Asp Pro Met 1745 1750 1755 1760 Leu Ala Tyr Leu Gln Pro Phe Arg Thr Ser Arg Lys Lys Phe Leu Glu 1765 1770 1775 Val Pro Arg Phe Asp Lys Glu Asn Pro Phe Glu Gly Leu Asp Asp Ile 1780 1785 1790 Asn Leu Trp Ile Pro Leu Ser Glu Asn His Asp Ile Trp Ile Lys Thr 1795 1800 1805 Leu Thr Cys Ala Phe Leu Asp Ser Gly Gly Thr Lys Cys Glu Ile Leu 1810 1815 1820 Gln Leu Leu Lys Pro Met Cys Glu Val Lys Thr Asp Phe Cys Gln Thr 1825 1830 1835 1840 Val Leu Pro Tyr Leu Ile His Asp Ile Leu Leu Gln Asp Thr Asn Glu 1845 1850 1855 Ser Trp Arg Asn Leu Leu Ser Thr His Val Gln Gly Phe Phe Thr Ser 1860 1865 1870 Cys Leu Arg His Phe Ser Gln Thr Ser Arg Ser Thr Thr Pro Ala Asn 1875 1880 1885 Leu Asp Ser Glu Ser Glu His Phe Phe Arg Cys Cys Leu Asp Lys Lys 1890 1895 1900 Ser Gln Arg Thr Met Leu Ala Val Val Asp Tyr Met Arg Arg Gln Lys 1905 1910 1915 1920 Arg Pro Ser Ser Gly Thr Ile Phe Asn Asp Ala Phe Trp Leu Asp Leu 1925 1930 1935 Asn Tyr Leu Glu Val Ala Lys Val Ala Gln Ser Cys Ala Ala His Phe 1940 1945 1950 Thr Ala Leu Leu Tyr Ala Glu Ile Tyr Ala Asp Lys Lys Ser Met Asp 1955 1960 1965 Asp Gln Glu Lys Arg Ser Leu Ala Phe Glu Glu Gly Ser Gln Ser Thr 1970 1975 1980 Thr Ile Ser Ser Leu Ser Glu Lys Ser Lys Glu Glu Thr Gly Ile Ser 1985 1990 1995 2000 Leu Gln Asp Leu Leu Leu Glu Ile Tyr Arg Ser Ile Gly Glu Pro Asp 2005 2010 2015 Ser Leu Tyr Gly Cys Gly Gly Gly Lys Met Leu Gln Pro Ile Thr Arg 2020 2025 2030 Leu Arg Thr Tyr Glu His Glu Ala Met Trp Gly Lys Ala Leu Val Thr 2035 2040 2045 Tyr Asp Leu Glu Thr Ala Ile Pro Ser Ser Thr Arg Gln Ala Gly Ile 2050 2055 2060 Ile Gln Ala Leu Gln Asn Leu Gly Leu Cys His Ile Leu Ser Val Tyr 2065 2070 2075 2080 Leu Lys Gly Leu Asp Tyr Glu Asn Lys Asp Trp Cys Pro Glu Leu Glu 2085 2090 2095 Glu Leu His Tyr Gln Ala Ala Trp Arg Asn Met Gln Trp Asp His Cys 2100 2105 2110 Thr Ser Val Ser Lys Glu Val Glu Gly Thr Ser Tyr His Glu Ser Leu 2115 2120 2125 Tyr Asn Ala Leu Gln Ser Leu Arg Asp Arg Glu Phe Ser Thr Phe Tyr 2130 2135 2140 Glu Ser Leu Lys Tyr Ala Arg Val Lys Glu Val Glu Glu Met Cys Lys 2145 2150 2155 2160 Arg Ser Leu Glu Ser Val Tyr Ser Leu Tyr Pro Thr Leu Ser Arg Leu 2165 2170 2175 Gln Ala Ile Gly Glu Leu Glu Ser Ile Gly Glu Leu Phe Ser Arg Ser 2180 2185 2190 Val Thr His Arg Gln Leu Ser Glu Val Tyr Ile Lys Trp Gln Lys His 2195 2200 2205 Ser Gln Leu Leu Lys Asp Ser Asp Phe Ser Phe Gln Glu Pro Ile Met 2210 2215 2220 Ala Leu Arg Thr Val Ile Leu Glu Ile Leu Met Glu Lys Glu Met Asp 2225 2230 2235 2240 Asn Ser Gln Arg Glu Cys Ile Lys Asp Ile Leu Thr Lys His Leu Val 2245 2250 2255 Glu Leu Ser Ile Leu Ala Arg Thr Phe Lys Asn Thr Gln Leu Pro Glu 2260 2265 2270 Arg Ala Ile Phe Gln Ile Lys Gln Tyr Asn Ser Val Ser Cys Gly Val 2275 2280 2285 Ser Glu Trp Gln Leu Glu Glu Ala Gln Val Phe Trp Ala Lys Lys Glu 2290 2295 2300 Gln Ser Leu Ala Leu Ser Ile Leu Lys Gln Met Ile Lys Lys Leu Asp 2305 2310 2315 2320 Ala Ser Cys Ala Ala Asn Asn Pro Ser Leu Lys Leu Thr Tyr Thr Glu 2325 2330 2335 Cys Leu Arg Val Cys Gly Asn Trp Leu Ala Glu Thr Cys Leu Glu Asn 2340 2345 2350 Pro Ala Val Ile Met Gln Thr Tyr Leu Glu Lys Ala Val Glu Val Ala 2355 2360 2365 Gly Asn Tyr Asp Gly Glu Ser Ser Asp Glu Leu Arg Asn Gly Lys Met 2370 2375 2380 Lys Ala Phe Leu Ser Leu Ala Arg Phe Ser Asp Thr Gln Tyr Gln Arg 2385 2390 2395 2400 Ile Glu Asn Tyr Met Lys Ser Ser Glu Phe Glu Asn Lys Gln Ala Leu 2405 2410 2415 Leu Lys Arg Ala Lys Glu Glu Val Gly Leu Leu Arg Glu His Lys Ile 2420 2425 2430 Gln Thr Asn Arg Tyr Thr Val Lys Val Gln Arg Glu Leu Glu Leu Asp 2435 2440 2445 Glu Leu Ala Leu Arg Ala Leu Lys Glu Asp Arg Lys Arg Phe Leu Cys 2450 2455 2460 Lys Ala Val Glu Asn Tyr Ile Asn Cys Leu Leu Ser Gly Glu Glu His 2465 2470 2475 2480 Asp Met Trp Val Phe Arg Leu Cys Ser Leu Trp Leu Glu Asn Ser Gly 2485 2490 2495 Val Ser Glu Val Asn Gly Met Met Lys Arg Asp Gly Met Lys Ile Pro 2500 2505 2510 Thr Tyr Lys Phe Leu Pro Leu Met Tyr Gln Leu Ala Ala Arg Met Gly 2515 2520 2525 Thr Lys Met Met Gly Gly Leu Gly Phe His Glu Val Leu Asn Asn Leu 2530 2535 2540 Ile Ser Arg Ile Ser Met Asp His Pro His His Thr Leu Phe Ile Ile 2545 2550 2555 2560 Leu Ala Leu Ala Asn Ala Asn Arg Asp Glu Phe Leu Thr Lys Pro Glu 2565 2570 2575 Val Ala Arg Arg Ser Arg Ile Thr Lys Asn Val Pro Lys Gln Ser Ser 2580 2585 2590 Gln Leu Asp Glu Asp Arg Thr Glu Ala Ala Asn Arg Ile Ile Cys Thr 2595 2600 2605 Ile Arg Ser Arg Arg Pro Gln Met Val Arg Ser Val Glu Ala Leu Cys 2610 2615 2620 Asp Ala Tyr Ile Ile Leu Ala Asn Leu Asp Ala Thr Gln Trp Lys Thr 2625 2630 2635 2640 Gln Arg Lys Gly Ile Asn Ile Pro Ala Asp Gln Pro Ile Thr Lys Leu 2645 2650 2655 Lys Asn Leu Glu Asp Val Val Val Pro Thr Met Glu Ile Lys Val Asp 2660 2665 2670 His Thr Gly Glu Tyr Gly Asn Leu Val Thr Ile Gln Ser Phe Lys Ala 2675 2680 2685 Glu Phe Arg Leu Ala Gly Gly Val Asn Leu Pro Lys Ile Ile Asp Cys 2690 2695 2700 Val Gly Ser Asp Gly Lys Glu Arg Arg Gln Leu Val Lys Gly Arg Asp 2705 2710 2715 2720 Asp Leu Arg Gln Asp Ala Val Met Gln Gln Val Phe Gln Met Cys Asn 2725 2730 2735 Thr Leu Leu Gln Arg Asn Thr Glu Thr Arg Lys Arg Lys Leu Thr Ile 2740 2745 2750 Cys Thr Tyr Lys Val Val Pro Leu Ser Gln Arg Ser Gly Val Leu Glu 2755 2760 2765 Trp Cys Thr Gly Thr Val Pro Ile Gly Glu Phe Leu Val Asn Asn Glu 2770 2775 2780 Asp Gly Ala His Lys Arg Tyr Arg Pro Asn Asp Phe Ser Ala Phe Gln 2785 2790 2795 2800 Cys Gln Lys Lys Met Met Glu Val Gln Lys Lys Ser Phe Glu Glu Lys 2805 2810 2815 Tyr Glu Val Phe Met Asp Val Cys Gln Asn Phe Gln Pro Val Phe Arg 2820 2825 2830 Tyr Phe Cys Met Glu Lys Phe Leu Asp Pro Ala Ile Trp Phe Glu Lys 2835 2840 2845 Arg Leu Ala Tyr Thr Arg Ser Val Ala Thr Ser Ser Ile Val Gly Tyr 2850 2855 2860 Ile Leu Gly Leu Gly Asp Arg His Val Gln Asn Ile Leu Ile Asn Glu 2865 2870 2875 2880 Gln Ser Ala Glu Leu Val His Ile Asp Leu Gly Val Ala Phe Glu Gln 2885 2890 2895 Gly Lys Ile Leu Pro Thr Pro Glu Thr Val Pro Phe Arg Leu Thr Arg 2900 2905 2910 Asp Ile Val Asp Gly Met Gly Ile Thr Gly Val Glu Gly Val Phe Arg 2915 2920 2925 Arg Cys Cys Glu Lys Thr Met Glu Val Met Arg Asn Ser Gln Glu Thr 2930 2935 2940 Leu Leu Thr Ile Val Glu Val Leu Leu Tyr Asp Pro Leu Phe Asp Trp 2945 2950 2955 2960 Thr Met Asn Pro Leu Lys Ala Leu Tyr Leu Gln Gln Arg Pro Glu Asp 2965 2970 2975 Glu Thr Glu Leu His Pro Thr Leu Asn Ala Asp Asp Gln Glu Cys Lys 2980 2985 2990 Arg Asn Leu Ser Asp Ile Asp Gln Ser Phe Asp Lys Val Ala Glu Arg 2995 3000 3005 Val Leu Met Arg Leu Gln Glu Lys Leu Lys Gly Val Glu Glu Gly Thr 3010 3015 3020 Val Leu Ser Val Gly Gly Gln Val Asn Leu Leu Ile Gln Gln Ala Ile 3025 3030 3035 3040 Asp Pro Lys Asn Leu Ser Arg Leu Phe Pro Gly Trp Lys Ala Trp Val 3045 3050 3055

Claims

What is claimed is:

1. A method for predicting a predisposition to breast cancer in an individual comprising:

determining the presence of an alteration in the germline A-T nucleic acid sequence from said individual as compared to the wildtype germline A-T nucleic acid sequence, wherein the germline alteration is an A-T susceptibility allele statistically associated with a predisposition to breast cancer.

2. The method of claim 1, wherein determining the presence of an alteration in the germline A-T nucleic acid sequence further comprises the steps of:

obtaining a sample which contains nucleic acid from said individual;

screening for the presence of said germline A-T nucleic acid sequence in said sample;

sequencing said germline A-T nucleic acid sequence in said sample; and

determining the presence of an alteration in said germline A-T nucleic acid sequence.

3. The method of claim 2, wherein said nucleic acid is DNA selected from the group consisting of cDNA, ssDNA, dsDNA, and genomic DNA.

4. The method of claim 2, wherein said nucleic acid is RNA selected from the group consisting of mRNA, dsRNA, and ssRNA.

5. The method of claim 2, wherein said determining the presence of an alteration is performed by one or more methods selected from the group consisting of direct DNA sequencing, SSCA, CDGE, HA, CMC, DGGE, RNase protection assays, ASOs, and allele-specific PCR.

6. The method of claim 2, wherein said sample comprises a human tissue.

7. The method of claim 2, wherein said sample comprises a human cell type.

8. The method of claim 2, wherein said sample is a biological sample.

9. The method of claim 1, wherein said alteration comprises a mutation in said germline A-T nucleic acid sequence.

10. The method of claim 9, wherein said mutation occurs in the coding region of said germline A-T nucleic acid sequence.

11. The method of claim 9, wherein said mutation is one or more selected from the group consisting of point mutations, insertions, and deletions.

12. The method of claim 9, wherein said mutation in said germline A-T nucleic acid sequence is selected from the group the group consisting of 3245 ATC→TGAT, 8269 del 150, 2689 del 5, 1402 del AA, 1027 del GAAA, and 9003 TTT-C.